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comparison sistr_cmd.xml @ 5:24a7a95867b0 draft default tip

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"planemo upload commit 683b11f79a83cf9e1563e46a75919157fa1136d4"
author nml
date Fri, 19 Mar 2021 20:09:37 +0000
parents 17fcac7ddf54
children
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4:17fcac7ddf54 5:24a7a95867b0
1 <tool id="sistr_cmd" name="sistr_cmd" version="@VERSION@"> 1 <tool id="sistr_cmd" name="sistr_cmd" version="@VERSION@+galaxy1">
2 <description> 2 <description>
3 Salmonella In Silico Typing Resource commandline tool for serovar prediction 3 Salmonella In Silico Typing Resource commandline tool for serovar prediction
4 </description> 4 </description>
5 <macros> 5 <macros>
6 <token name="@VERSION@">1.1.1</token> 6 <token name="@VERSION@">1.1.1</token>
12 <exit_code range="1:" /> 12 <exit_code range="1:" />
13 </stdio> 13 </stdio>
14 <command><![CDATA[ 14 <command><![CDATA[
15 sistr 15 sistr
16 #for $fasta in $input_fastas 16 #for $fasta in $input_fastas
17 -i '$fasta' '${$fasta.name.replace("." + $fasta.ext, "")}' 17 -i '$fasta' '${$fasta.element_identifier.replace("." + $fasta.ext, "")}'
18 #end for 18 #end for
19 -f $output_format 19 -f $output_format
20 -o sistr-report.$output_format 20 -o sistr-report.$output_format
21 -p $cgmlst_profiles 21 -p $cgmlst_profiles
22 -n $novel_alleles 22 -n $novel_alleles
37 type="data" 37 type="data"
38 label="Input Genome(s)" 38 label="Input Genome(s)"
39 optional="false" 39 optional="false"
40 multiple="true" 40 multiple="true"
41 format="fasta" 41 format="fasta"
42 /> 42 />
43 <param 43 <param
44 name="output_format" 44 name="output_format"
45 type="select" 45 type="select"
46 label="Results output format" 46 label="Results output format"
47 multiple="false"> 47 multiple="false">