Mercurial > repos > thanhlv > amrfinderplus
changeset 2:a9e5d593228e draft default tip
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/ncbi-armfinderplus commit 2c3091cc8850849ac99884f92f195e4de9774f99
author | thanhlv |
---|---|
date | Wed, 11 Sep 2019 09:51:28 -0400 |
parents | f92ab7729a35 |
children | |
files | amrfinderplus.xml |
diffstat | 1 files changed, 7 insertions(+), 8 deletions(-) [+] |
line wrap: on
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--- a/amrfinderplus.xml Tue Sep 10 12:32:19 2019 -0400 +++ b/amrfinderplus.xml Wed Sep 11 09:51:28 2019 -0400 @@ -29,7 +29,7 @@ -g '$input_selection.gff.gff_file' #end if #end if - #if str($organism) != 'none' + #if str($organism) != 'None' -O $organism #end if -o results.tsv @@ -87,7 +87,6 @@ </options> </param> <param name="organism" type="select" optional="true" label="Get organism-specific results"> - <option value="none" selected="true">None</option> <option value="Campylobacter">Campylobacter</option> <option value="Escherichia">Escherichia</option> <option value="Klebsiella">Klebsiella</option> @@ -112,13 +111,13 @@ <tests> <test> <!-- dna input--> - <param name="input_selection|input_source_selector" value="nuc"/> + <param name="input_source_selector" value="nuc"/> <param name="fasta_file" value="test_dna.fa" ftype="fasta"/> <param name="amrfinder_databases" value="2019-08-27.1" /> <output name="result" file="test_dna.expected" lines_diff="1"/> </test> <test> <!-- dna input and organism, plus gene--> - <param name="input_selection|input_source_selector" value="nuc"/> + <param name="input_source_selector" value="nuc"/> <param name="fasta_file" value="test_dna.fa" ftype="fasta"/> <param name="organism" value="Escherichia" /> <param name="plus" value="true" /> @@ -126,17 +125,17 @@ <output name="result" file="test_dna_Escherichia.expected" lines_diff="1"/> </test> <test> <!-- AA input--> - <param name="input_selection|input_source_selector" value="pro"/> + <param name="input_source_selector" value="pro"/> <param name="fasta_file" value="test_prot.fa" ftype="fasta"/> <param name="amrfinder_databases" value="2019-08-27.1" /> <output name="result" file="test_prot.expected" lines_diff="1"/> </test> <test> <!-- DNA and AA input--> - <param name="input_selection|input_source_selector" value="both"/> - <param name="input_selection|input_source_selector|gff|use" value="gff_yes"/> + <param name="input_source_selector" value="both"/> + <param name="use" value="gff_yes"/> <param name="nuc_file" value="test_dna.fa" ftype="fasta"/> <param name="pro_file" value="test_prot.fa" ftype="fasta"/> - <param name="input_selection|gff|use" value="gff_yes"/> + <param name="use" value="gff_yes"/> <param name="gff_file" value="test_prot.gff" ftype="gff3"/> <param name="amrfinder_databases" value="2019-08-27.1" /> <output name="result" file="test_both.expected" lines_diff="1"/>