Mercurial > repos > jpayne > snp_pipeline
annotate 4_merge_sites.xml @ 11:772f310d2506
planemo upload commit 7f6183b769772449fbcee903686b8d5ec5b7439f-dirty
| author | jpayne |
|---|---|
| date | Tue, 30 Jan 2018 17:15:09 -0500 |
| parents | 25b858c2f21d |
| children | 8764af78e270 |
| 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@0 | 6 <requirement type="package">snp-pipeline</requirement> |
| jpayne@10 | 7 <requirement type="package" version="3.4">python3</requirement> |
| jpayne@0 | 8 </requirements> |
| jpayne@0 | 9 <command detect_errors="exit_code"><![CDATA[ |
| jpayne@9 | 10 python $__tool_directory__/snp-wind.py ./ |
| jpayne@0 | 11 #for $call in $calls |
| jpayne@0 | 12 -n $call.element_identifier -f $call |
| jpayne@0 | 13 #end for |
| jpayne@0 | 14 -p "var.fit.vcf" > ./file |
| jpayne@0 | 15 && cfsan_snp_pipeline merge_sites -v 4 -n "var.fit.vcf" ./file ./filtered_snps -o $snplist |
| jpayne@0 | 16 ]]></command> |
| jpayne@0 | 17 <inputs> |
| jpayne@0 | 18 <param type="data_collection" name="calls" format="vcf" collection_type="list" /> |
| jpayne@0 | 19 </inputs> |
| jpayne@0 | 20 <outputs> |
| jpayne@0 | 21 <data name="snplist" format="txt" /> |
| jpayne@0 | 22 </outputs> |
| jpayne@0 | 23 <tests> |
| jpayne@0 | 24 <test> |
| jpayne@0 | 25 <param name="calls"> |
| jpayne@0 | 26 <collection type="list"> |
| jpayne@0 | 27 <element name="sample1" value="samples/sample1/var.flt_preserved.vcf" /> |
| jpayne@0 | 28 <element name="sample2" value="samples/sample2/var.flt_preserved.vcf" /> |
| jpayne@0 | 29 <element name="sample3" value="samples/sample3/var.flt_preserved.vcf" /> |
| jpayne@0 | 30 <element name="sample4" value="samples/sample4/var.flt_preserved.vcf" /> |
| jpayne@0 | 31 </collection> |
| jpayne@0 | 32 </param> |
| jpayne@0 | 33 <!-- <output name="snplist" value="snplist.txt" /> --> |
| jpayne@0 | 34 </test> |
| jpayne@0 | 35 </tests> |
| jpayne@0 | 36 <help><![CDATA[ |
| jpayne@0 | 37 <a href="http://snp-pipeline.readthedocs.io/en/latest/index.html">http://snp-pipeline.readthedocs.io/en/latest/index.html</a> |
| jpayne@0 | 38 ]]></help> |
| jpayne@0 | 39 <citations> |
| jpayne@0 | 40 <citation type="doi">10.7717/peerj-cs.20</citation> |
| jpayne@0 | 41 </citations> |
| jpayne@0 | 42 </tool> |