amrfinderplus_db: amrfinderplus

annotate amrfinderplus_db.xml @ 7:de2011569700 draft default tip

planemo upload commit 50e7d8610c04e06eb15f09131d6a2d1b204de6a9

author	galaxytrakr
date	Fri, 13 Mar 2026 15:43:54 +0000
parents	01549d36ad56
children

rev	line source
0 06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	1 <tool id="amrfinderplus_db" name="AMRFinderPlus" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	2 <description>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	3 NCBI Antimicrobial Resistance Gene Finder
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	4 </description>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	5 <macros>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	6 <import>macro.xml</import>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	7 </macros>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	8 <expand macro="biotools"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	9 <expand macro="requirements"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	10 <expand macro="version_command"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	11 <command detect_errors="aggressive"><![CDATA[
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	12 amrfinder
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	13 #*======================================
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	14 CPU option
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	15 ======================================*#
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	16 --threads \${GALAXY_SLOTS:-1}
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	17 #*======================================
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	18 DATABASE
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	19 ======================================*#
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	20 --database '$input_option.amrfinder_db_select.fields.path'
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	21 #*======================================
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	22 INPUT TYPE
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	23 ======================================*#
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	24 #if $input_option.input_mode.input_select == 'nucleotide'
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	25 --nucleotide $input_option.input_mode.nucleotide_input
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	26 #if $input_option.input_mode.nucleotide_flank5_size > 0
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	27 --nucleotide_flank5_size $input_option.input_mode.nucleotide_flank5_size
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	28 --nucleotide_flank5_output 'amrfinderplus_flanking_sequence_output.fasta'
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	29 #end if
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	30 --nucleotide_output 'amrfinderplus_nucleotide_output.fasta'
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	31 #elif $input_option.input_mode.input_select == 'protein'
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	32 --protein $input_option.input_mode.protein_input
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	33 #if $input_option.input_mode.gff_annotation
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	34 --gff $input_option.input_mode.gff_annotation
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	35 #end if
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	36 #if $input_option.input_mode.annotation_format
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	37 --annotation_format $input_option.input_mode.annotation_format
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	38 #end if
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	39 --protein_output 'amrfinderplus_protein_output.fasta'
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	40 #else
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	41 --nucleotide $input_option.input_mode.nucleotide_input
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	42 #if $input_option.input_mode.nucleotide_flank5_size and $input_option.input_mode.nucleotide_flank5_size > 0
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	43 --nucleotide_flank5_size $input_option.input_mode.nucleotide_flank5_size
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	44 --nucleotide_flank5_output 'amrfinderplus_flanking_sequence_output.fasta'
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	45 #end if
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	46 --protein $input_option.input_mode.protein_input
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	47 --gff $input_option.input_mode.gff_annotation
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	48 --annotation_format $input_option.input_mode.annotation_format
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	49 --nucleotide_output 'amrfinderplus_nucleotide_output.fasta'
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	50 --protein_output 'amrfinderplus_protein_output.fasta'
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	51 #end if
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	52 #*======================================
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	53 ORGANISM PART
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	54 ======================================*#
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	55 #if $organism_options.organism_conditionnal.organism_select
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	56 --organism '$organism_options.organism_conditionnal.organism'
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	57 #if $organism_options.organism_conditionnal.mutation_all
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	58 $organism_options.organism_conditionnal.mutation_all 'mutation_all_report.tsv'
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	59 #end if
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	60 #if $options.plus
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	61 $organism_options.organism_conditionnal.report_common
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	62 #end if
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	63 #end if
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	64 #*======================================
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	65 OPTIONS
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	66 ======================================*#
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	67 --ident_min '$options.ident_min'
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	68 --coverage_min '$options.coverage_min'
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	69 #if '$options.translation_table'
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	70 --translation_table '$options.translation_table'
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	71 #end if
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	72 #if '$options.name'
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	73 --name '$options.name'
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	74 #end if
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	75 $options.plus
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	76 $options.report_all_equal
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	77 $options.print_node
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	78 --output 'amrfinderplus_report.tsv'
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	79
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	80 ]]></command>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	81 <inputs>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	82
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	83 <section name="input_option" title="Input/Output options" expanded="true">
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	84 <param name="amrfinder_db_select" type="select" label="The amrfinderplus database">
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	85 <options from_data_table="amrfinderplus_versioned_database">
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	86 </options>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	87 </param>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	88 <conditional name="input_mode">
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	89 <param name="input_select" type="select" label="Choose input type" help="Choose the type of files (nucleotide and/or protein to be analyzed)">
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	90 <option value="nucleotide">Nucleotide</option>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	91 <option value="protein">Protein</option>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	92 <option value="nucl_prot">Nucleotide and Protein</option>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	93 </param>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	94 <when value="nucleotide">
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	95 <expand macro="nucl_input" option="false"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	96 <param argument="--nucleotide_flank5_size" optional="true" type="integer" min="0" value="0" label="5' flanking sequence size added with sequence match"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	97 </when>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	98 <when value="protein">
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	99 <expand macro="prot_input" option="false"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	100 <expand macro="annotation_type" option="true"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	101 </when>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	102 <when value="nucl_prot">
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	103 <expand macro="nucl_input" option="false"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	104 <expand macro="prot_input" option="false"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	105 <expand macro="annotation_type" option="false"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	106 <param argument="--nucleotide_flank5_size" optional="true" type="integer" min="0" value="0" label="5' flanking sequence size added with sequence match"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	107 </when>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	108 </conditional>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	109 </section>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	110 <!-- ORGANISM OPTIONS -->
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	111 <section name="organism_options" title="Organism options">
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	112 <conditional name="organism_conditionnal">
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	113 <param name="organism_select" type="select" label="Add organism specifications">
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	114 <option value="" selected="true">No specifications</option>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	115 <option value="add_organism">Add organism specifications</option>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	116 </param>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	117 <when value="add_organism">
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	118 <param argument="--organism" type="select" optional="false" label="Taxonomy group point mutation" help="Choose a taxonomic group to point mutation screening">
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	119 <option value="Acinetobacter_baumannii">Acinetobacter_baumannii</option>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	120 <option value="Burkholderia_cepacia">Burkholderia_cepacia</option>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	121 <option value="Burkholderia_pseudomallei">Burkholderia_pseudomallei</option>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	122 <option value="Campylobacter">Campylobacter</option>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	123 <option value="Citrobacter_freundii">Citrobacter_freundii</option>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	124 <option value="Clostridioides_difficile">Clostridioides_difficile</option>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	125 <option value="Enterobacter_cloacae">Enterobacter_cloacae</option>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	126 <option value="Enterococcus_faecalis">Enterococcus_faecalis</option>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	127 <option value="Enterococcus_faecium">Enterococcus_faecium</option>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	128 <option value="Escherichia">Escherichia</option>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	129 <option value="Klebsiella_aerogenes">Klebsiella_aerogenes</option>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	130 <option value="Klebsiella_oxytoca">Klebsiella_oxytoca</option>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	131 <option value="Klebsiella_pneumoniae">Klebsiella_pneumoniae</option>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	132 <option value="Neisseria_gonorrhoeae">Neisseria_gonorrhoeae</option>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	133 <option value="Neisseria_meningitidis">Neisseria_meningitidis</option>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	134 <option value="Pseudomonas_aeruginosa">Pseudomonas_aeruginosa</option>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	135 <option value="Salmonella">Salmonella</option>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	136 <option value="Serratia_marcescens">Serratia_marcescens</option>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	137 <option value="Staphylococcus_aureus">Staphylococcus_aureus</option>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	138 <option value="Staphylococcus_pseudintermedius">Staphylococcus_pseudintermedius</option>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	139 <option value="Streptococcus_agalactiae">Streptococcus_agalactiae</option>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	140 <option value="Streptococcus_pneumoniae">Streptococcus_pneumoniae</option>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	141 <option value="Streptococcus_pyogenes">Streptococcus_pyogenes</option>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	142 <option value="Vibrio_cholerae">Vibrio_cholerae</option>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	143 </param>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	144 <param argument="--mutation_all" type="boolean" truevalue="--mutation_all" falsevalue="" label="Report genotypes at all locations screened for point mutations"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	145 <param argument="--report_common" type="boolean" truevalue="--report_common" falsevalue=""
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	146 label="Report proteins common to a taxonomy group (need the plus and organism options)"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	147 </when>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	148 <when value="">
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	149 </when>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	150 </conditional>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	151 </section>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	152 <!-- OPTIONS -->
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	153 <section name="options" title="Options">
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	154 <param argument="--ident_min" type="float" min="-1" max="1" value="-1" label="Minimum identity"
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	155 help="Minimum proportion of identical amino acids in alignment. -1 means use a curated threshold if it exists and 0.9 otherwise (default: -1)"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	156 <param argument="--coverage_min" type="float" min="0" max="1" value="0.5" label="Minimum coverage"
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	157 help="Minimum coverage of the reference protein (0 to 1, default: 0.5)"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	158 <param argument="--translation_table" type="select" optional="true" label="Translation table" help="NCBI genetic code for translated BLAST (default: bacterial table 11)">
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	159 <option value="1">1 Standard code</option>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	160 <option value="2">2 Vertebrate mitochondrial</option>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	161 <option value="3">3 Yeast mitochondrial</option>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	162 <option value="4">4 Mold, Protozoan, and Coelenterate Mitochondrial and the Mycoplasma/Spiroplasma</option>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	163 <option value="5">5 Invertebrate mitochondrial</option>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	164 <option value="6">6 Ciliate, dasycladacean and hexamita nuclear</option>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	165 <option value="9">9 Echinoderm and flatworm mitochondrial</option>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	166 <option value="10">10 Euplotid nuclear</option>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	167 <option value="11" selected="true">11 Bacterial, Archaeal and Plant Plastid</option>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	168 <option value="12">12 Alternative yeast nuclear</option>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	169 <option value="13">13 Ascidian mitochondrial</option>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	170 <option value="14">14 Alternative flatworm mitochondrial</option>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	171 <option value="16">16 Chlorophycean mitochondrial</option>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	172 <option value="21">21 Trematode Mitochondrial</option>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	173 <option value="22">22 Scenedesmus obliquus Mitochondrial</option>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	174 <option value="23">23 Thraustochytrium Mitochondrial</option>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	175 <option value="24">24 Rhabdopleuridae Mitochondrial</option>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	176 <option value="25">25 Candidate Division SR1 and Gracilibacteria</option>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	177 <option value="26">26 Pachysolen tannophilus Nuclear</option>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	178 <option value="27">27 Karyorelict Nuclear</option>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	179 <option value="28">28 Condylostoma Nuclear</option>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	180 <option value="29">29 Mesodinium nuclear</option>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	181 <option value="30">30 Peritrich nuclear</option>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	182 <option value="31">31 Blastocrithidia nuclear</option>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	183 <option value="33">33 Cephalodiscidae mitochondrial</option>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	184 </param>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	185 <param argument="--plus" type="boolean" truevalue="--plus" falsevalue="" label="Add the plus genes to the report"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	186 <param argument="--report_all_equal" type="boolean" truevalue="--report_all_equal" falsevalue="" label="Report all equally-scoring BLAST and HMM matches"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	187 <param argument="--print_node" type="boolean" truevalue="--print_node" falsevalue="" label="print hierarchy node (family)"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	188 <param argument="--name" type="text" label="First column name" help="Text to be added as the first column 'name' to all rows of the report"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	189 </section>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	190 </inputs>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	191 <outputs>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	192 <data name="amrfinderplus_report" format="tabular" from_work_dir="amrfinderplus_report.tsv" label="${tool.name} on ${on_string}: AMRFinderPlus report"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	193 <data name="mutation_all_report" format="tabular" from_work_dir="mutation_all_report.tsv" label="${tool.name} on ${on_string}: Point mutation report">
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	194 <filter> organism_options['organism_conditionnal']['organism_select'] == "add_organism" and organism_options['organism_conditionnal']['mutation_all'] is True </filter>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	195 </data>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	196 <data name="protein_output" format="fasta" from_work_dir="amrfinderplus_protein_output.fasta" label="${tool.name} on ${on_string}: Protein identified sequences">
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	197 <filter> input_option['input_mode']['input_select'] in ['protein', 'nucl_prot']</filter>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	198 </data>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	199 <data name="nucleotide_output" format="fasta" from_work_dir="amrfinderplus_nucleotide_output.fasta" label="${tool.name} on ${on_string}: Nucleotide identified sequences">
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	200 <filter> input_option['input_mode']['input_select'] in ['nucleotide', 'nucl_prot'] </filter>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	201 </data>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	202 <data name="nucleotide_flank5_output" format="fasta" from_work_dir="amrfinderplus_flanking_sequence_output.fasta"
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	203 label="${tool.name} on ${on_string}: Nucleotide sequences with 5' flanking regions">
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	204 <filter> input_option['input_mode']['input_select'] in ['nucleotide', 'nucl_prot'] and input_option['input_mode']['nucleotide_flank5_size'] != 0 </filter>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	205 </data>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	206 </outputs>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	207 <tests>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	208 <test expect_num_outputs="2"> <!-- TEST_1 simple nucleotide input -->
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	209 <section name="input_option">
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	210 <param name="amrfinder_db_select" value="V3.12-2024-05-02.2"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	211 <conditional name="input_mode">
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	212 <param name="input_select" value="nucleotide"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	213 <param name="nucleotide_input" value="enterococcus_faecalis.fna"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	214 </conditional>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	215 </section>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	216 <output name="amrfinderplus_report" ftype="tabular">
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	217 <assert_contents>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	218 <has_n_columns n="22"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	219 <has_n_lines n="8"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	220 <has_text text="optrA"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	221 <has_text text="WP_063854496"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	222 <has_text text="WP_063843211"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	223 </assert_contents>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	224 </output>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	225 <output name="nucleotide_output" ftype="fasta">
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	226 <assert_contents>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	227 <has_n_lines n="142"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	228 <has_text text=">contig_26:6581-8545 strand:+ optrA ABC-F type ribosomal protection protein OptrA"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	229 <has_text text="TTGTCCAAAGCC"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	230 </assert_contents>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	231 </output>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	232 </test>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	233 <test expect_num_outputs="3"> <!-- TEST_2 nucleotide input and full options -->
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	234 <section name="input_option">
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	235 <param name="amrfinder_db_select" value="V3.12-2024-05-02.2"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	236 <conditional name="input_mode">
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	237 <param name="input_select" value="nucleotide"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	238 <param name="nucleotide_input" value="enterococcus_faecalis.fna"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	239 <param name="nucleotide_flank5_size" value="150"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	240 </conditional>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	241 </section>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	242 <section name="organism_options">
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	243 <conditional name="organism_conditionnal">
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	244 <param name="organism_select" value="add_organism"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	245 <param name="organism" value="Enterococcus_faecalis"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	246 <param name="report_common" value="true"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	247 </conditional>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	248 </section>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	249 <section name="options">
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	250 <param name="ident_min" value="0.1"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	251 <param name="coverage_min" value="0.1"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	252 <param name="translation_table" value="11"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	253 <param name="plus" value="true"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	254 <param name="report_all_equal" value="true"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	255 <param name="print_node" value="true"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	256 <param name="name" value="test_2"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	257 <param name="log" value="true"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	258 </section>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	259 <output name="amrfinderplus_report" ftype="tabular">
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	260 <assert_contents>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	261 <has_n_columns n="24"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	262 <has_n_lines n="13"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	263 <has_text text="optrA"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	264 <has_text text="WP_063854496"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	265 </assert_contents>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	266 </output>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	267 <output name="nucleotide_output" ftype="fasta">
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	268 <assert_contents>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	269 <has_n_lines n="267"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	270 <has_text text=">contig_26:6581-8545 strand:+ optrA ABC-F type ribosomal protection protein OptrA"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	271 <has_text text="TTGTCCAAAGCC"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	272 </assert_contents>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	273 </output>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	274 <output name="nucleotide_flank5_output" ftype="fasta">
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	275 <assert_contents>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	276 <has_n_lines n="298"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	277 <has_text text=">contig_2:54987-57395 strand:- mupB mupirocin-resistant isoleucine--tRNA ligase MupB"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	278 <has_text text="TTGTCCAAAGCC"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	279 </assert_contents>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	280 </output>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	281 </test>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	282 <test expect_num_outputs="2"> <!-- TEST_3 nucleotide input and several options -->
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	283 <section name="input_option">
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	284 <param name="amrfinder_db_select" value="V3.12-2024-05-02.2"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	285 <conditional name="input_mode">
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	286 <param name="input_select" value="nucleotide"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	287 <param name="nucleotide_input" value="enterococcus_faecalis.fna"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	288 </conditional>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	289 </section>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	290 <section name="organism_options">
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	291 <conditional name="organism_conditionnal">
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	292 <param name="organism_select" value="add_organism"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	293 <param name="organism" value="Enterococcus_faecalis"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	294 <param name="report_common" value="true"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	295 </conditional>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	296 </section>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	297 <section name="options">
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	298 <param name="report_all_equal" value="true"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	299 </section>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	300 <output name="amrfinderplus_report" ftype="tabular">
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	301 <assert_contents>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	302 <has_n_columns n="22"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	303 <has_n_lines n="9"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	304 <has_text text="optrA"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	305 <has_text text="WP_063854496"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	306 <has_text text="WP_063856080"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	307 </assert_contents>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	308 </output>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	309 <output name="nucleotide_output" ftype="fasta">
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	310 <assert_contents>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	311 <has_n_lines n="142"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	312 <has_text text=">contig_26:6581-8545 strand:+ optrA ABC-F type ribosomal protection protein OptrA"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	313 <has_text text="TTGTCCAAAGCC"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	314 </assert_contents>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	315 </output>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	316 </test>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	317 <test expect_num_outputs="2"> <!-- TEST_4 simple protein input -->
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	318 <section name="input_option">
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	319 <param name="amrfinder_db_select" value="V3.12-2024-05-02.2"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	320 <conditional name="input_mode">
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	321 <param name="input_select" value="protein"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	322 <param name="protein_input" value="enterococcus_faecalis.faa"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	323 </conditional>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	324 </section>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	325 <output name="amrfinderplus_report" ftype="tabular">
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	326 <assert_contents>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	327 <has_n_columns n="18"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	328 <has_n_lines n="7"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	329 <has_text text="optrA"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	330 <has_text text="WP_063854496"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	331 <has_text text="WP_063856080"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	332 </assert_contents>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	333 </output>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	334 <output name="protein_output" ftype="fasta">
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	335 <assert_contents>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	336 <has_n_lines n="49"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	337 <has_text text=">IDOBJL_14770 aph(3')-IIIa aminoglycoside O-phosphotransferase APH(3')-IIIa"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	338 <has_text text="SDYIVLTEIQKSIDDVKRCQGNYF"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	339 </assert_contents>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	340 </output>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	341 </test>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	342 <test expect_num_outputs="2"> <!-- TEST_5 protein input and full options to gff3 and bakta -->
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	343 <section name="input_option">
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	344 <param name="amrfinder_db_select" value="V3.12-2024-05-02.2"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	345 <conditional name="input_mode">
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	346 <param name="input_select" value="protein"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	347 <param name="protein_input" value="enterococcus_faecalis.faa"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	348 <param name="gff_annotation" value="enterococcus_faecalis_bakta.gff3"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	349 <param name="annotation_format" value="bakta"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	350 </conditional>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	351 </section>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	352 <section name="organism_options">
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	353 <conditional name="organism_conditionnal">
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	354 <param name="organism_select" value="add_organism"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	355 <param name="organism" value="Enterococcus_faecalis"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	356 <param name="report_common" value="true"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	357 </conditional>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	358 </section>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	359 <section name="options">
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	360 <param name="ident_min" value="0.1"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	361 <param name="coverage_min" value="0.4"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	362 <param name="translation_table" value="11"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	363 <param name="plus" value="true"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	364 <param name="report_all_equal" value="true"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	365 <param name="print_node" value="true"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	366 <param name="name" value="test_5"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	367 </section>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	368 <output name="amrfinderplus_report" ftype="tabular">
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	369 <assert_contents>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	370 <has_n_columns n="24"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	371 <has_n_lines n="8"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	372 <has_text text="optrA"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	373 <has_text text="IDOBJL_14770"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	374 <has_text text="WP_063856080"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	375 </assert_contents>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	376 </output>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	377 <output name="nucleotide_output" ftype="fasta">
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	378 <assert_contents>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	379 <has_n_lines n="49"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	380 <has_text text=">IDOBJL_14770 aph(3')-IIIa aminoglycoside O-phosphotransferase APH(3')-IIIa"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	381 <has_text text="SDYIVLTEIQKSIDDVKRCQGNYF"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	382 </assert_contents>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	383 </output>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	384 </test>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	385 <test expect_num_outputs="2"> <!-- TEST_6 protein input and prokka annotation -->
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	386 <section name="input_option">
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	387 <param name="amrfinder_db_select" value="V3.12-2024-05-02.2"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	388 <conditional name="input_mode">
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	389 <param name="input_select" value="protein"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	390 <param name="protein_input" value="PROKKA_05252023.faa"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	391 <param name="gff_annotation" value="PROKKA_05252023.gff"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	392 <param name="annotation_format" value="prokka"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	393 </conditional>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	394 </section>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	395 <output name="amrfinderplus_report" ftype="tabular">
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	396 <assert_contents>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	397 <has_n_columns n="22"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	398 <has_n_lines n="7"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	399 <has_text text="FODBOAIN_02586"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	400 <has_text text="WP_063856395"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	401 </assert_contents>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	402 </output>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	403 <output name="protein_output" ftype="fasta">
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	404 <assert_contents>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	405 <has_n_lines n="49"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	406 <has_text text=">FODBOAIN_02586 optrA ABC-F type ribosomal protection protein OptrA"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	407 <has_text text="YSNLLLLFSGIIVISWLVTLNVYKHSQRDF"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	408 </assert_contents>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	409 </output>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	410 </test>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	411 <test expect_num_outputs="2"> <!-- TEST_7 protein input and genbank default annotation -->
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	412 <section name="input_option">
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	413 <param name="amrfinder_db_select" value="V3.12-2024-05-02.2"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	414 <conditional name="input_mode">
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	415 <param name="input_select" value="protein"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	416 <param name="protein_input" value="input_ncbi.faa"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	417 <param name="gff_annotation" value="annotation_ncbi.gff3"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	418 </conditional>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	419 </section>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	420 <output name="amrfinderplus_report" ftype="tabular">
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	421 <assert_contents>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	422 <has_n_columns n="22"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	423 <has_n_lines n="4"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	424 <has_text text="blaOXA"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	425 <has_text text="WP_063855540"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	426 </assert_contents>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	427 </output>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	428 <output name="protein_output" ftype="fasta">
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	429 <assert_contents>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	430 <has_n_lines n="17"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	431 <has_text text=">blaOXA-436_partial blaOXA OXA-48 family class D beta-lactamase"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	432 <has_text text="SSNPDAAPVSS"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	433 </assert_contents>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	434 </output>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	435 </test>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	436 <test expect_num_outputs="3"> <!-- TEST_8 both protein and nucleotide input -->
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	437 <section name="input_option">
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	438 <param name="amrfinder_db_select" value="V3.12-2024-05-02.2"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	439 <conditional name="input_mode">
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	440 <param name="input_select" value="nucl_prot"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	441 <param name="protein_input" value="enterococcus_faecalis.faa"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	442 <param name="nucleotide_input" value="enterococcus_faecalis.fna"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	443 <param name="gff_annotation" value="enterococcus_faecalis_bakta.gff3"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	444 <param name="annotation_format" value="bakta"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	445 </conditional>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	446 </section>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	447 <section name="organism_options">
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	448 <conditional name="organism_conditionnal">
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	449 <param name="organism_select" value="add_organism"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	450 <param name="organism" value="Enterococcus_faecalis"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	451 </conditional>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	452 </section>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	453 <output name="amrfinderplus_report" ftype="tabular">
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	454 <assert_contents>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	455 <has_n_columns n="22"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	456 <has_n_lines n="8"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	457 <has_text text="IDOBJL_14770"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	458 <has_text text="WP_063856080"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	459 </assert_contents>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	460 </output>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	461 <output name="nucleotide_output" ftype="fasta">
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	462 <assert_contents>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	463 <has_n_lines n="143"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	464 <has_text text=">contig_26:6581-8545 strand:+ optrA ABC-F type ribosomal protection protein OptrA"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	465 <has_text text="CTTATCTGTATAG"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	466 </assert_contents>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	467 </output>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	468 <output name="protein_output" ftype="fasta">
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	469 <assert_contents>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	470 <has_n_lines n="37"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	471 <has_text text=">IDOBJL_14770 aph(3')-IIIa aminoglycoside O-phosphotransferase APH(3')-IIIa"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	472 <has_text text="QEAGAGMSLLNFT"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	473 </assert_contents>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	474 </output>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	475 </test>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	476 <test expect_num_outputs="4"> <!-- TEST_9 rast annotation and mutation all results -->
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	477 <section name="input_option">
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	478 <param name="amrfinder_db_select" value="V3.12-2024-05-02.2"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	479 <conditional name="input_mode">
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	480 <param name="input_select" value="nucl_prot"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	481 <param name="protein_input" value="e_faecalis_rast.faa"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	482 <param name="nucleotide_input" value="e_faecalis_rast.fna"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	483 <param name="gff_annotation" value="e_faecalis_rast.gff"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	484 <param name="annotation_format" value="rast"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	485 </conditional>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	486 </section>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	487 <section name="organism_options">
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	488 <conditional name="organism_conditionnal">
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	489 <param name="organism_select" value="add_organism"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	490 <param name="organism" value="Enterococcus_faecalis"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	491 <param name="mutation_all" value="true"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	492 </conditional>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	493 </section>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	494 <section name="options">
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	495 <param name="ident_min" value="0.1"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	496 <param name="coverage_min" value="0.1"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	497 <param name="plus" value="true"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	498 <param name="print_node" value="true"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	499 <param name="name" value="test_5"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	500 </section>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	501 <output name="amrfinderplus_report" ftype="tabular">
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	502 <assert_contents>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	503 <has_n_columns n="24"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	504 <has_n_lines n="2"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	505 <has_text text="MUPIROCIN"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	506 <has_text text="WP_063854488"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	507 </assert_contents>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	508 </output>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	509 <output name="nucleotide_output" ftype="fasta">
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	510 <assert_contents>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	511 <has_n_lines n="40"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	512 <has_text text=">contig00019:27227-29524 strand:+ mupB mupirocin-resistant isoleucine--tRNA ligase MupB"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	513 <has_text text="ATCAGTCGTGAAATAGAA"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	514 </assert_contents>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	515 </output>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	516 <output name="protein_output" ftype="fasta">
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	517 <assert_contents>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	518 <has_n_lines n="0"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	519 </assert_contents>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	520 </output>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	521 <output name="mutation_all_report" ftype="tabular">
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	522 <assert_contents>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	523 <has_n_columns n="24"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	524 <has_n_lines n="5"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	525 <has_text text="23S_GA375AG"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	526 <has_text text="NZ_CP04"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	527 </assert_contents>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	528 </output>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	529 </test>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	530 </tests>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	531 <help><![CDATA[
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	532 What it does
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	533
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	534 AMRFinderPlus is a tool to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences.
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	535
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	536 Input file analysis
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	537
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	538 AMRFinderPlus can check in nucleotide and/or protein fasta file
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	539 When protein file is provided, sensitivity is higher if you add an annotation file
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	540
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	541 Organism options
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	542
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	543 With organism informations AMRFinderPlus screens known resistance causing point mutations and blacklisting of common, non-informative genes.
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	544
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	545 The mutation_all option make a new output file containing all detected variants from the reference sequence.
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	546
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	547 This file allows you to distinguish between called point mutations that were the sensitive variant and the point mutations that could not be called because the sequence was not found.
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	548
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	549 +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	550 \| Organism option \| Point mutations \| Blacklisted plus genes \| Notes \|
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	551 +=================================+==================+=============================+============================================================+
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	552 \| Acinetobacter_baumannii \| X \| \| Use for the A. baumannii-calcoaceticus species complex \|
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	553 +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	554 \| Burkholderia_cepacia \| X \| \| Use for the Burkholderia cepacia species complex \|
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	555 +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	556 \| Burkholderia_pseudomallei \| X \| \| Use for the Burkholderia pseudomallei species complex \|
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	557 +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	558 \| Campylobacter \| X \| \| Use for C. coli and C. jejuni \|
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	559 +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	560 \| Citrobacter_freundii \| X \| \| \|
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	561 +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	562 \| Clostridioides_difficile \| X \| \| \|
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	563 +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	564 \| Enterobacter_cloacae \| X \| \| \|
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	565 +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	566 \| Enterococcus_faecalis \| X \| \| \|
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	567 +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	568 \| Enterococcus_faecium \| X \| \| Use for E. hirae \|
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	569 +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	570 \| Escherichia \| X \| X \| Use for Shigella and Escherichia \|
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	571 +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	572 \| Klebsiella_oxytoca \| X \| X \| \|
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	573 +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	574 \| Klebsiella_pneumoniae \| X \| X \| Use for K. pneumoniae species complex and K. aerogenes \|
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	575 +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	576 \| Neisseria_gonorrhoeae \| X \| \| \|
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	577 +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	578 \| Neisseria_meningitidis \| X \| \| \|
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	579 +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	580 \| Pseudomonas_aeruginosa \| X \| \| \|
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	581 +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	582 \| Salmonella \| X \| X \| \|
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	583 +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	584 \| Serratia_marcescens \| X \| \| \|
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	585 +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	586 \| Staphylococcus_aureus \| X \| \| \|
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	587 +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	588 \| Staphylococcus_pseudintermedius \| X \| X \| \|
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	589 +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	590 \| Streptococcus_agalactiae \| X \| \| \|
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	591 +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	592 \| Streptococcus_pneumoniae \| X \| \| Use for S. pneumoniae and S. mitis \|
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	593 +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	594 \| Streptococcus_pyogenes \| X \| \| \|
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	595 +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	596 \| Vibrio_cholerae \| X \| \| \|
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	597 +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	598
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	599
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	600 Supplementary options
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	601 - nucleotide 5' flanking size to extract nucleotide matches and a range of nucleotide in 5'
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	602 - Minimum identity to choose threshold in amino acids alignemnt. -1 for a high curation threshold.
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	603 - Minimum coverage Coverage to protein alignment.
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	604 - Translation table by default AMRFinderPlus work on bacteria but can be modified to some other Phyla.
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	605 - Plus option provide more information related to virulence, stress response ...
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	606
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	607 Output files
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	608
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	609 AMRFinderPlus can generate some differents files :
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	610 - The AMRFinderPlus report with identified protein, gene and AMR related informations.
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	611 - A report with all detected variants from the reference sequence.
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	612 - The protein and/ort nucleotide matched sequences.
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	613 - Only when nucleotide a nucleotide fasta file could be provided with 5' flanking regions.
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	614
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	615
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	616 ]]></help>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	617 <expand macro="citations"/>
06165bd8c9a0 planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8 estrain parents: diff changeset	618 </tool>

Mercurial > repos > estrain > amrfinderplus_db

annotate amrfinderplus_db.xml @ 7:de2011569700 draft default tip