Mercurial > repos > nml > sistr_cmd

comparison sistr_cmd.xml @ 1:9d7e381dfa5a draft

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planemo upload commit 9d3d0b2dc47cc803e560e396e5c13d2cfef9ed03
author nml
date Fri, 03 Mar 2017 14:31:21 -0500
parents ebee10be4297
children 13632190a0ff
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0:ebee10be4297 1:9d7e381dfa5a
12 sistr 12 sistr
13 #for $fasta in $input_fastas 13 #for $fasta in $input_fastas
14 -i '$fasta' '${$fasta.name.replace("." + $fasta.ext, "")}' 14 -i '$fasta' '${$fasta.name.replace("." + $fasta.ext, "")}'
15 #end for 15 #end for
16 -f $output_format 16 -f $output_format
17 #if $output_format == "tab" 17 -o sistr-report.$output_format
18 -o sistr-report.tab
19 #elif $output_format == "csv"
20 -o sistr-report.csv
21 #elif $output_format == "json"
22 -o sistr-report.json
23 #end if
24 -p $cgmlst_profiles 18 -p $cgmlst_profiles
25 -n $novel_alleles 19 -n $novel_alleles
26 -a $alleles_output 20 -a $alleles_output
27 $use_full_cgmlst_db 21 $use_full_cgmlst_db
28 $no_cgmlst 22 $no_cgmlst