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comparison snippy-core.xml @ 5:f9d3b5a6ef31 draft

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"planemo upload commit b436c43bb4e8f28c91434173f1b8cb9b187056b2"
author iuc
date Thu, 12 Sep 2019 12:42:17 -0400
parents 98413117ca70
children 43791d945de1
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4:98413117ca70 5:f9d3b5a6ef31
1 <?xml version="1.0" encoding="utf-8"?> 1 <?xml version="1.0" encoding="utf-8"?>
2 <tool id="snippy_core" name="snippy-core" version="@VERSION@"> 2 <tool id="snippy_core" name="snippy-core" version="@VERSION@+galaxy0">
3 <description> 3 <description>
4 Combine multiple Snippy outputs into a core SNP alignment 4 Combine multiple Snippy outputs into a core SNP alignment
5 </description> 5 </description>
6 <macros> 6 <macros>
7 <import>macros.xml</import> 7 <import>macros.xml</import>
8 </macros> 8 </macros>
9 <expand macro="requirements" /> 9 <expand macro="requirements" />
10 <command detect_errors="exit_code"><![CDATA[ 10 <command detect_errors="exit_code"><![CDATA[
11 @REFERENCE_SOURCE_FILE@
11 #for $indir in $indirs 12 #for $indir in $indirs
12 #set $sample_name = os.path.splitext(os.path.basename(str($indir.name)))[0] 13 #set $sample_name = os.path.splitext(os.path.basename(str($indir.name)))[0]
13 mkdir '$sample_name' && tar -xf '$indir' -C '$sample_name' --strip-components=1 && 14 mkdir '$sample_name' && tar -xf '$indir' -C '$sample_name' --strip-components=1 &&
14 #end for 15 #end for
15 #set snippy_dirs = " ".join(["'{0}'".format(os.path.splitext(os.path.basename(str($indir.name)))[0]) for $indir in $indirs]) 16 #set snippy_dirs = " ".join(["'{0}'".format(os.path.splitext(os.path.basename(str($indir.name)))[0]) for $indir in $indirs])
16 snippy-core 17 snippy-core
17 --ref '$ref' 18 @REFERENCE_COMMAND@
18 ${snippy_dirs} 19 ${snippy_dirs}
19 ]]></command> 20 ]]></command>
20 21
21 <inputs> 22 <inputs>
22 <param name="indirs" type="data" multiple="true" format="zip" label="Snippy input zipped dirs" help="Select all the snippy inputs for alignment" /> 23 <param name="indirs" type="data" multiple="true" format="zip" label="Snippy input zipped dirs" help="Select all the snippy inputs for 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" /> 24 <expand macro="reference_selector" />
24 <param name="outputs" type="select" multiple="true" display="checkboxes" label="Output selection"> 25 <param name="outputs" type="select" multiple="true" display="checkboxes" label="Output selection">
25 <option value="outaln" selected="True">A core SNP alignment in the fasta format</option> 26 <option value="outaln" selected="True">A core SNP alignment in the fasta format</option>
26 <option value="outfull" selected="False">A whole genome SNP alignment (includes invariant sites)</option> 27 <option value="outfull" selected="False">A whole genome SNP alignment (includes invariant sites)</option>
27 <option value="outtab" selected="False">Tab-separated columnar list of core SNP sites with alleles and annotations</option> 28 <option value="outtab" selected="False">Tab-separated columnar list of core SNP sites with alleles and annotations</option>
28 <option value="outtxt" selected="False">Tab-separated columnar list of alignment/core-size statistics</option> 29 <option value="outtxt" selected="False">Tab-separated columnar list of alignment/core-size statistics</option>
46 </outputs> 47 </outputs>
47 48
48 <tests> 49 <tests>
49 <test><!-- Test #1 - test with 3 zipped directories --> 50 <test><!-- Test #1 - test with 3 zipped directories -->
50 <param name="indirs" value="a.tgz,b.tgz,c.tgz" /> 51 <param name="indirs" value="a.tgz,b.tgz,c.tgz" />
51 <param name="ref" value="reference.fasta" /> 52 <conditional name="reference_source">
53 <param name="reference_source_selector" value="history"/>
54 <param name="ref_file" value="reference.fasta" ftype="fasta"/>
55 </conditional>
56 <param name="outputs" value="outtxt" />
57 <output name="alignment_summary" ftype="txt" file="a_b_c.core.txt" />
58 </test>
59 <test><!-- Test #2 - test with 3 zipped directories -->
60 <param name="indirs" value="a.tgz,b.tgz,c.tgz" />
61 <conditional name="reference_source">
62 <param name="reference_source_selector" value="cached"/>
63 <param name="ref_file" value="test_id"/>
64 </conditional>
52 <param name="outputs" value="outtxt" /> 65 <param name="outputs" value="outtxt" />
53 <output name="alignment_summary" ftype="txt" file="a_b_c.core.txt" /> 66 <output name="alignment_summary" ftype="txt" file="a_b_c.core.txt" />
54 </test> 67 </test>
55 </tests> 68 </tests>
56 69