annotate 4_merge_sites.xml @ 28:1d77f9fb51f3

planemo upload commit 7f6183b769772449fbcee903686b8d5ec5b7439f-dirty
author jpayne
date Wed, 31 Jan 2018 13:34:32 -0500 (2018-01-31)
parents 8764af78e270
children 87f53c4a13df
rev   line source
jpayne@0 1 <tool id="merge_sites" name="4. Merge Sites" version="1.0.1" profile="16.10">
jpayne@0 2 <description>from multiple samples</description>
jpayne@0 3 <requirements>
jpayne@0 4 <requirement type="package" version="2.2.6">bowtie2</requirement>
jpayne@0 5 <requirement type="package" version="1.2">samtools</requirement>
jpayne@12 6 <requirement type="package" version="1.0.6">bzip2</requirement>
jpayne@0 7 <requirement type="package">snp-pipeline</requirement>
jpayne@10 8 <requirement type="package" version="3.4">python3</requirement>
jpayne@0 9 </requirements>
jpayne@0 10 <command detect_errors="exit_code"><![CDATA[
jpayne@9 11 python $__tool_directory__/snp-wind.py ./
jpayne@0 12 #for $call in $calls
jpayne@0 13 -n $call.element_identifier -f $call
jpayne@0 14 #end for
jpayne@0 15 -p "var.fit.vcf" > ./file
jpayne@0 16 && cfsan_snp_pipeline merge_sites -v 4 -n "var.fit.vcf" ./file ./filtered_snps -o $snplist
jpayne@0 17 ]]></command>
jpayne@0 18 <inputs>
jpayne@0 19 <param type="data_collection" name="calls" format="vcf" collection_type="list" />
jpayne@0 20 </inputs>
jpayne@0 21 <outputs>
jpayne@0 22 <data name="snplist" format="txt" />
jpayne@0 23 </outputs>
jpayne@0 24 <tests>
jpayne@0 25 <test>
jpayne@0 26 <param name="calls">
jpayne@0 27 <collection type="list">
jpayne@0 28 <element name="sample1" value="samples/sample1/var.flt_preserved.vcf" />
jpayne@0 29 <element name="sample2" value="samples/sample2/var.flt_preserved.vcf" />
jpayne@0 30 <element name="sample3" value="samples/sample3/var.flt_preserved.vcf" />
jpayne@0 31 <element name="sample4" value="samples/sample4/var.flt_preserved.vcf" />
jpayne@0 32 </collection>
jpayne@0 33 </param>
jpayne@0 34 <!-- <output name="snplist" value="snplist.txt" /> -->
jpayne@0 35 </test>
jpayne@0 36 </tests>
jpayne@0 37 <help><![CDATA[
jpayne@0 38 <a href="http://snp-pipeline.readthedocs.io/en/latest/index.html">http://snp-pipeline.readthedocs.io/en/latest/index.html</a>
jpayne@0 39 ]]></help>
jpayne@0 40 <citations>
jpayne@0 41 <citation type="doi">10.7717/peerj-cs.20</citation>
jpayne@0 42 </citations>
jpayne@0 43 </tool>