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comparison 4_merge_sites.xml @ 0:eefdd97a6749

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planemo upload commit b'7f6183b769772449fbcee903686b8d5ec5b7439f\n'-dirty
author jpayne
date Wed, 24 Jan 2018 14:18:21 -0500
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1 <tool id="merge_sites" name="4. Merge Sites" version="1.0.1" profile="16.10">
2 <description>from multiple samples</description>
3 <requirements>
4 <requirement type="package" version="2.2.6">bowtie2</requirement>
5 <requirement type="package" version="1.2">samtools</requirement>
6 <requirement type="package">snp-pipeline</requirement>
7 </requirements>
8 <command detect_errors="exit_code"><![CDATA[
9 $__tool_directory__/snp-wind.py ./
10 #for $call in $calls
11 -n $call.element_identifier -f $call
12 #end for
13 -p "var.fit.vcf" > ./file
14 && cfsan_snp_pipeline merge_sites -v 4 -n "var.fit.vcf" ./file ./filtered_snps -o $snplist
15 ]]></command>
16 <inputs>
17 <param type="data_collection" name="calls" format="vcf" collection_type="list" />
18 </inputs>
19 <outputs>
20 <data name="snplist" format="txt" />
21 </outputs>
22 <tests>
23 <test>
24 <param name="calls">
25 <collection type="list">
26 <element name="sample1" value="samples/sample1/var.flt_preserved.vcf" />
27 <element name="sample2" value="samples/sample2/var.flt_preserved.vcf" />
28 <element name="sample3" value="samples/sample3/var.flt_preserved.vcf" />
29 <element name="sample4" value="samples/sample4/var.flt_preserved.vcf" />
30 </collection>
31 </param>
32 <!-- <output name="snplist" value="snplist.txt" /> -->
33 </test>
34 </tests>
35 <help><![CDATA[
36 <a href="http://snp-pipeline.readthedocs.io/en/latest/index.html">http://snp-pipeline.readthedocs.io/en/latest/index.html</a>
37 ]]></help>
38 <citations>
39 <citation type="doi">10.7717/peerj-cs.20</citation>
40 </citations>
41 </tool>