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comparison snippy-core.xml @ 2:776ebd1239da draft

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planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496
author iuc
date Mon, 18 Mar 2019 10:59:29 -0400
parents c9a8ef2aa380
children 9bccc8404a3c
comparison
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1:82f2b6f20fa2 2:776ebd1239da
1 <?xml version="1.0" encoding="utf-8"?>
1 <tool id="snippy_core" name="snippy-core" version="@VERSION@"> 2 <tool id="snippy_core" name="snippy-core" version="@VERSION@">
2 <description> 3 <description>
3 Combine multiple Snippy outputs into a core SNP alignment 4 Combine multiple Snippy outputs into a core SNP alignment
4 </description> 5 </description>
5 <macros> 6 <macros>
6 <import>macros.xml</import> 7 <import>macros.xml</import>
7 </macros> 8 </macros>
8 <expand macro="requirements" /> 9 <expand macro="requirements" />
9 <command detect_errors="exit_code"><![CDATA[ 10 <command detect_errors="exit_code"><![CDATA[
10 11 #for $indir in $indirs
11 perl '$__tool_directory__/snippy_core_wrapper.pl' 12 #set $sample_name = os.path.splitext(os.path.basename(str($indir.name)))[0]
12 '$is_reference' 13 mkdir '$sample_name' && tar -xf '$indir' -C '$sample_name' --strip-components=1 &&
13 --indirs '${" ".join(map(str, $indirs))}' 14 #end for
14 15 #set snippy_dirs = ' '.join([os.path.splitext(os.path.basename(str($indir.name)))[0] for $indir in $indirs])
16 snippy-core
17 --ref '$ref'
18 ${snippy_dirs}
15 ]]></command> 19 ]]></command>
16 20
17 <inputs> 21 <inputs>
18 <param name="indirs" type="data" multiple="true" format="zip" label="Snippy input zipped dirs" help="Select all the snippy inputs for alignment" /> 22 <param name="indirs" type="data" multiple="true" format="zip" label="Snippy input zipped dirs" help="Select all the snippy inputs for alignment" />
19 <param name="is_reference" type="boolean" checked="true" truevalue="--noref" falsevalue="" label="Exclude reference" help="Don't include the reference file in the alignment." /> 23 <param name="ref" type="data" format="fasta,genbank" label="Reference File (either in fasta or genbank format)" help="Fasta or Genbank file to use as the reference" />
20 <param name="outputs" type="select" multiple="true" display="checkboxes" label="Output selection"> 24 <param name="outputs" type="select" multiple="true" display="checkboxes" label="Output selection">
21 <option value="outaln" selected="True">A core SNP alignment in the fasta format</option> 25 <option value="outaln" selected="True">A core SNP alignment in the fasta format</option>
22 <option value="outfull" selected="False">A whole genome SNP alignment (includes invariant sites)</option> 26 <option value="outfull" selected="False">A whole genome SNP alignment (includes invariant sites)</option>
23 <option value="outtab" selected="False">Tab-separated columnar list of core SNP sites with alleles and annotations</option> 27 <option value="outtab" selected="False">Tab-separated columnar list of core SNP sites with alleles and annotations</option>
24 <option value="outtxt" selected="False">Tab-separated columnar list of alignment/core-size statistics</option> 28 <option value="outtxt" selected="False">Tab-separated columnar list of alignment/core-size statistics</option>
40 <filter>outputs and 'outtxt' in outputs</filter> 44 <filter>outputs and 'outtxt' in outputs</filter>
41 </data> 45 </data>
42 </outputs> 46 </outputs>
43 47
44 <tests> 48 <tests>
45 <test><!-- Test #1 - test with 2 zipped directories --> 49 <test><!-- Test #1 - test with 3 zipped directories -->
46 <param name="indirs" value="S1.tgz,S2.tgz" /> 50 <param name="indirs" value="a.tgz,b.tgz,c.tgz" />
47 <param name="is_reference" value="false" /> 51 <param name="ref" value="reference.fasta" />
48 <param name="outputs" value="outtxt" /> 52 <param name="outputs" value="outtxt" />
49 <output name="alignment_summary" ftype="txt" file="core/core.txt" /> 53 <output name="alignment_summary" ftype="txt" file="a_b_c.core.txt" />
50 </test> 54 </test>
51 </tests> 55 </tests>
52 56
53 <help><![CDATA[ 57 <help><![CDATA[
54 **snippy-core @VERSION@** 58 **snippy-core @VERSION@**
69 **Note:** 73 **Note:**
70 74
71 snippy **must** have been run with --cleanup False 75 snippy **must** have been run with --cleanup False
72 76
73 ]]></help> 77 ]]></help>
74
75 <expand macro="citations" /> 78 <expand macro="citations" />
76 </tool> 79 </tool>