Mercurial > repos > estrain > ncbi_amrfinderplus

annotate amrfinderplus.xml @ 1:f28db31c50d8

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author estrain
date Fri, 06 Mar 2020 10:41:43 -0500
parents 2089a8f9e732
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estrain@0 1 <tool id="amrfinder" name="amrfinder" version="@VERSION@+galaxy1">
estrain@0 2 <description>
estrain@0 3 identifies AMR genes using either protein annotations or nucleotide sequence.
estrain@0 4 </description>
estrain@0 5 <macros>
estrain@0 6 <token name="@VERSION@">3.6.10</token>
estrain@0 7 </macros>
estrain@0 8 <requirements>
estrain@0 9 <requirement type="package" version="@VERSION@">ncbi-amrfinderplus</requirement>
estrain@0 10 </requirements>
estrain@0 11 <version_command><![CDATA[amrfinder --version]]></version_command>
estrain@0 12
estrain@0 13 <command detect_errors="exit_code"><![CDATA[
estrain@0 14 amrfinder
estrain@0 15 $plus
estrain@0 16 --threads \${GALAXY_SLOTS:-1}
estrain@0 17 --database '$amrfinder_databases.fields.path'
estrain@0 18 #if $input_selection.input_source_selector == 'nuc'
estrain@0 19 -n '$input_selection.fasta_file'
estrain@0 20 #elif $input_selection.input_source_selector == 'pro'
estrain@0 21 -p '$input_selection.fasta_file'
estrain@0 22 #if $input_selection.gff.use == 'gff_yes'
estrain@0 23 -g '$input_selection.gff.gff_file'
estrain@0 24 #end if
estrain@0 25 #elif $input_selection.input_source_selector == 'both'
estrain@0 26 -n '$input_selection.nuc_file'
estrain@0 27 -p '$input_selection.pro_file'
estrain@0 28 #if $input_selection.gff.use == 'gff_yes'
estrain@0 29 -g '$input_selection.gff.gff_file'
estrain@0 30 #end if
estrain@0 31 #end if
estrain@0 32 #if str($organism) != 'None'
estrain@0 33 -O $organism
estrain@0 34 #end if
estrain@0 35 -o results.tsv
estrain@0 36 $report_common
estrain@0 37 #if $point_mut_all
estrain@0 38 --point_mut_all point_mutate.tsv
estrain@0 39 #end if
estrain@0 40 $gpipe
estrain@0 41 ]]> </command>
estrain@0 42
estrain@0 43 <inputs>
estrain@0 44 <conditional name="input_selection">
estrain@0 45 <param name="input_source_selector" type="select" label="Input data type">
estrain@0 46 <option value="nuc">Nucleotide</option>
estrain@0 47 <option value="pro">Protein</option>
estrain@0 48 <option value="both">Nucleotide and Protein</option>
estrain@0 49 </param>
estrain@0 50 <when value="nuc">
estrain@0 51 <param name="fasta_file" type="data" format="fasta" label="Select nucleotide fasta file"/>
estrain@0 52 </when>
estrain@0 53 <when value="pro">
estrain@0 54 <param name="fasta_file" type="data" format="fasta" label="Select protein fasta file"/>
estrain@0 55 <conditional name="gff">
estrain@0 56 <param name="use" type="select" label="Using GFF to get genomic coordinates">
estrain@0 57 <option value="gff_yes">Yes</option>
estrain@0 58 <option value="gff_no" selected="true">No</option>
estrain@0 59 </param>
estrain@0 60 <when value="gff_yes">
estrain@0 61 <param name="gff_file" type="data" format="gff,gff3" label="Select GFF file" help="Protein id should be in the attribute 'Name=id' (9th field) of the rows with type 'CDS' or 'gene' (3rd field)."/>
estrain@0 62 </when>
estrain@0 63 <when value="gff_no">
estrain@0 64 </when>
estrain@0 65 </conditional>
estrain@0 66 </when>
estrain@0 67 <when value="both">
estrain@0 68 <param name="nuc_file" type="data" format="fasta" label="Select a nucleotide fasta file"/>
estrain@0 69 <param name="pro_file" type="data" format="fasta" label="Select a protein fasta file"/>
estrain@0 70 <conditional name="gff">
estrain@0 71 <param name="use" type="select" label="Using GFF to get genomic coordinates">
estrain@0 72 <option value="gff_yes">Yes</option>
estrain@0 73 <option value="gff_no" selected="true">No</option>
estrain@0 74 </param>
estrain@0 75 <when value="gff_yes">
estrain@0 76 <param name="gff_file" type="data" format="gff,gff3" label="Select GFF file" help="Protein id should be in the attribute 'Name=id' (9th field) of the rows with type 'CDS' or 'gene' (3rd field)."/>
estrain@0 77 </when>
estrain@0 78 <when value="gff_no">
estrain@0 79 </when>
estrain@0 80 </conditional>
estrain@0 81 </when>
estrain@0 82 </conditional>
estrain@0 83 <!-- DATABASE INPUT-->
estrain@0 84 <param name="amrfinder_databases" label="Select a database" type="select">
estrain@0 85 <options from_data_table="amrfinder_databases">
estrain@0 86 <validator message="No database is available" type="no_options" />
estrain@0 87 </options>
estrain@0 88 </param>
estrain@0 89 <param name="organism" type="select" optional="true" label="Get organism-specific results">
estrain@0 90 <option value="Campylobacter">Campylobacter</option>
estrain@0 91 <option value="Escherichia">Escherichia</option>
estrain@0 92 <option value="Klebsiella">Klebsiella</option>
estrain@0 93 <option value="Salmonella">Salmonella</option>
estrain@0 94 <option value="Staphylococcus">Staphylococcus</option>
estrain@0 95 <option value="Vibrio">Vibrio</option>
estrain@0 96 </param>
estrain@0 97 <param name="min_iden" argument="--ident_min" type="float" value="-1" label="Minimum identity for a blast-based hit" help="(Methods BLAST or PARTIAL). -1 means use a curated threshold if it exists and 0.9 otherwise. Setting this value to something other than -1 will override any curated similarity cutoffs" />
estrain@0 98 <param name="min_cov" argument="--coverage_min" type="float" min="0" max="1" value="0.5" label="Minimum coverage of the reference protein" />
estrain@0 99 <param name="plus" type="boolean" truevalue="--plus" falsevalue="" label="Add the plus genes to the report" />
estrain@0 100 <param name="report_common" type="boolean" truevalue="--report_common" falsevalue="" label="Suppress proteins common to a taxonomy group" />
estrain@0 101 <param name="point_mut_all" type="boolean" truevalue="true" falsevalue="false" label="Report all target positions of reference point mutations" />
estrain@0 102 <param name="gpipe" type="boolean" truevalue="--gpipe" falsevalue="" label="Protein identifiers in the protein FASTA file have format gnl-project-accession" />
estrain@0 103 </inputs>
estrain@0 104
estrain@0 105 <outputs>
estrain@0 106 <data name="result" format="tabular" from_work_dir="results.tsv" label="${tool.name} on ${on_string}: Result"/>
estrain@0 107 <data name="point_mutate" format="tabular" from_work_dir="point_mutate.tsv" label="${tool.name} on ${on_string}: Point mutate all">
estrain@0 108 <filter>point_mut_all</filter>
estrain@0 109 </data>
estrain@0 110 </outputs>
estrain@0 111
estrain@0 112 <tests>
estrain@0 113 <test> <!-- dna input-->
estrain@0 114 <param name="input_source_selector" value="nuc"/>
estrain@0 115 <param name="fasta_file" value="test_dna.fa" ftype="fasta"/>
estrain@0 116 <param name="amrfinder_databases" value="2019-08-27.1" />
estrain@0 117 <output name="result" file="test_dna.expected" lines_diff="1"/>
estrain@0 118 </test>
estrain@0 119 <test> <!-- dna input and organism, plus gene-->
estrain@0 120 <param name="input_source_selector" value="nuc"/>
estrain@0 121 <param name="fasta_file" value="test_dna.fa" ftype="fasta"/>
estrain@0 122 <param name="organism" value="Escherichia" />
estrain@0 123 <param name="plus" value="true" />
estrain@0 124 <param name="amrfinder_databases" value="2019-08-27.1" />
estrain@0 125 <output name="result" file="test_dna_Escherichia.expected" lines_diff="1"/>
estrain@0 126 </test>
estrain@0 127 <test> <!-- AA input-->
estrain@0 128 <param name="input_source_selector" value="pro"/>
estrain@0 129 <param name="fasta_file" value="test_prot.fa" ftype="fasta"/>
estrain@0 130 <param name="amrfinder_databases" value="2019-08-27.1" />
estrain@0 131 <output name="result" file="test_prot.expected" lines_diff="1"/>
estrain@0 132 </test>
estrain@0 133 <test> <!-- DNA and AA input-->
estrain@0 134 <param name="input_source_selector" value="both"/>
estrain@0 135 <param name="use" value="gff_yes"/>
estrain@0 136 <param name="nuc_file" value="test_dna.fa" ftype="fasta"/>
estrain@0 137 <param name="pro_file" value="test_prot.fa" ftype="fasta"/>
estrain@0 138 <param name="use" value="gff_yes"/>
estrain@0 139 <param name="gff_file" value="test_prot.gff" ftype="gff3"/>
estrain@0 140 <param name="amrfinder_databases" value="2019-08-27.1" />
estrain@0 141 <output name="result" file="test_both.expected" lines_diff="1"/>
estrain@0 142 </test>
estrain@0 143 </tests>
estrain@0 144
estrain@0 145
estrain@0 146 <help><![CDATA[
estrain@0 147 This software and the accompanying database are designed to find acquired
estrain@0 148 antimicrobial resistance genes in bacterial protein or assembled nucleotide
estrain@0 149 sequences as well as known point mutations for several taxa. With
estrain@0 150 AMRFinderPlus we have added select members of additional classes of genes
estrain@0 151 such as virulence factors, biocide, heat, acid, and metal resistance genes.
estrain@0 152 More details: https://github.com/ncbi/amr/wiki
estrain@0 153 ]]> </help>
estrain@0 154 <citations>
estrain@0 155 <citation type="doi">10.1101/550707</citation>
estrain@0 156 </citations>
estrain@0 157
estrain@0 158 </tool>