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comparison Resfinder_wrapper.xml @ 3:a64cdbcf2407 draft

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author p.lucas
date Thu, 07 Apr 2022 12:25:02 +0000
parents 05f2df368f39
children 6010c8988869
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2:05f2df368f39 3:a64cdbcf2407
118 <requirement type="package" version="0.36.2">wheel</requirement> 118 <requirement type="package" version="0.36.2">wheel</requirement>
119 <requirement type="package" version="5.2.5">xz</requirement> 119 <requirement type="package" version="5.2.5">xz</requirement>
120 <requirement type="package" version="1.2.11">zlib</requirement> 120 <requirement type="package" version="1.2.11">zlib</requirement>
121 </requirements> 121 </requirements>
122 <command detect_errors="exit_code"><![CDATA[ 122 <command detect_errors="exit_code"><![CDATA[
123 python3 /home/galaxy/resfinder/run_resfinder.py -s "$s" -l "$l" -t "$y" --acquired --point -ifa ${input} -db_res /home/galaxy/resfinder/db_resfinder/ -db_point /home/galaxy/resfinder/db_pointfinder/ -o output && mv ./output/ResFinder_Resistance_gene_seq.fsa $resistance_genes 123 python3 /home/galaxy/resfinder/run_resfinder.py -s "$s" -l "$l" -t "$t" --acquired --point -ifa ${input} -db_res /home/galaxy/resfinder/db_resfinder/ -db_point /home/galaxy/resfinder/db_pointfinder/ -o output && mv ./output/ResFinder_Resistance_gene_seq.fsa $resistance_genes
124 ]]></command> 124 ]]></command>
125 <inputs> 125 <inputs>
126 <param format="fasta" name="input" type="data" label="FASTA file : "/> 126 <param format="fasta" name="input" type="data" label="FASTA file : "/>
127 <param name="s" type="select" label="Select the species:" help="*Chromosomal point mutation database exist"> 127 <param name="s" type="select" label="Select the species:" help="*Chromosomal point mutation database exist">
128 <option value="campylobacter">Campylobacter spp.*</option> 128 <option value="campylobacter">Campylobacter spp.*</option>