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comparison cfsan_snp_pipeline_merge_vcfs.xml @ 0:e958c5f7c9d1 draft

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author greg
date Wed, 22 Nov 2023 15:34:14 +0000
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1 <tool id="cfsan_snp_pipeline_merge_vcfs" name="CFSAN SNP Pipeline: merge vcfs" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>from multiple samples</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <command detect_errors="exit_code"><![CDATA[
8 python '$__tool_directory__/snp_wind.py' ./
9 #if str($input_type_cond.input_type) == 'single':
10 -n '$input_vcf.element_identifier'
11 -f '$input_vcf'
12 #else:
13 #for $input_vcf in $input_vcf_collection
14 -n '$input_vcf.element_identifier'
15 -f '$input_vcf'
16 #end for
17 #end if
18 -p 'consensus.vcf' > ./file
19 && cfsan_snp_pipeline merge_vcfs ./file
20 ]]></command>
21 <inputs>
22 <expand macro="input_type_cond"/>
23 </inputs>
24 <outputs>
25 <data name="output" format="vcf"/>
26 </outputs>
27 <tests>
28 <test>
29 <param name="input_type" value="collection"/>
30 <param name="input_vcf_collection">
31 <collection type="list">
32 <element name="sample1" value="samples/sample1/consensus.vcf" ftype="vcf"/>
33 <element name="sample2" value="samples/sample2/consensus.vcf" ftype="vcf"/>
34 <element name="sample3" value="samples/sample3/consensus.vcf" ftype="vcf"/>
35 <element name="sample4" value="samples/sample4/consensus.vcf" ftype="vcf"/>
36 </collection>
37 </param>
38 <output name="output" ftype="vcf">
39 <assert_contents>
40 <has_size value="0" delta="100"/>
41 </assert_contents>
42 </output>
43 </test>
44 </tests>
45 <help><![CDATA[
46 **What it does**
47
48 Merges the consensus vcf files from all samples into a single multi-vcf file.
49
50 **More information**
51
52 CFSAN SNP Pipeline `merge sites documentation <https://snp-pipeline.readthedocs.io/en/latest/cmd_ref.html#merge-sites>`_
53 ]]></help>
54 <expand macro="citations"/>
55 </tool>
56