# HG changeset patch
# User estrain
# Date 1773341616 0
# Node ID 06165bd8c9a019d7717c3e9f843f04e7ce91bccb
planemo upload commit 9ab7edbd247d0fbd4c7da45f4c77613720d1a3a8
diff -r 000000000000 -r 06165bd8c9a0 amrfinderplus_db.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/amrfinderplus_db.xml Thu Mar 12 18:53:36 2026 +0000
@@ -0,0 +1,618 @@
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+ NCBI Antimicrobial Resistance Gene Finder
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+ macro.xml
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+ 0
+ --nucleotide_flank5_size $input_option.input_mode.nucleotide_flank5_size
+ --nucleotide_flank5_output 'amrfinderplus_flanking_sequence_output.fasta'
+ #end if
+ --nucleotide_output 'amrfinderplus_nucleotide_output.fasta'
+ #elif $input_option.input_mode.input_select == 'protein'
+ --protein $input_option.input_mode.protein_input
+ #if $input_option.input_mode.gff_annotation
+ --gff $input_option.input_mode.gff_annotation
+ #end if
+ #if $input_option.input_mode.annotation_format
+ --annotation_format $input_option.input_mode.annotation_format
+ #end if
+ --protein_output 'amrfinderplus_protein_output.fasta'
+ #else
+ --nucleotide $input_option.input_mode.nucleotide_input
+ #if $input_option.input_mode.nucleotide_flank5_size and $input_option.input_mode.nucleotide_flank5_size > 0
+ --nucleotide_flank5_size $input_option.input_mode.nucleotide_flank5_size
+ --nucleotide_flank5_output 'amrfinderplus_flanking_sequence_output.fasta'
+ #end if
+ --protein $input_option.input_mode.protein_input
+ --gff $input_option.input_mode.gff_annotation
+ --annotation_format $input_option.input_mode.annotation_format
+ --nucleotide_output 'amrfinderplus_nucleotide_output.fasta'
+ --protein_output 'amrfinderplus_protein_output.fasta'
+ #end if
+ #*======================================
+ ORGANISM PART
+ ======================================*#
+ #if $organism_options.organism_conditionnal.organism_select
+ --organism '$organism_options.organism_conditionnal.organism'
+ #if $organism_options.organism_conditionnal.mutation_all
+ $organism_options.organism_conditionnal.mutation_all 'mutation_all_report.tsv'
+ #end if
+ #if $options.plus
+ $organism_options.organism_conditionnal.report_common
+ #end if
+ #end if
+ #*======================================
+ OPTIONS
+ ======================================*#
+ --ident_min '$options.ident_min'
+ --coverage_min '$options.coverage_min'
+ #if '$options.translation_table'
+ --translation_table '$options.translation_table'
+ #end if
+ #if '$options.name'
+ --name '$options.name'
+ #end if
+ $options.plus
+ $options.report_all_equal
+ $options.print_node
+ --output 'amrfinderplus_report.tsv'
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+ ]]>
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+ organism_options['organism_conditionnal']['organism_select'] == "add_organism" and organism_options['organism_conditionnal']['mutation_all'] is True
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+ input_option['input_mode']['input_select'] in ['protein', 'nucl_prot']
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+ input_option['input_mode']['input_select'] in ['nucleotide', 'nucl_prot']
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+ input_option['input_mode']['input_select'] in ['nucleotide', 'nucl_prot'] and input_option['input_mode']['nucleotide_flank5_size'] != 0
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diff -r 000000000000 -r 06165bd8c9a0 macro.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macro.xml Thu Mar 12 18:53:36 2026 +0000
@@ -0,0 +1,44 @@
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+ 4.2.5
+ 2
+ 21.05
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+ amrfinderplus
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+ ncbi-amrfinderplus
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+ 10.1038/s41598-021-91456-0
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