Mercurial > repos > jpayne > snp_pipeline
comparison 4_merge_sites.xml @ 58:d53281e6edae
planemo upload
| author | jpayne |
|---|---|
| date | Mon, 17 Jun 2024 02:57:10 -0400 |
| parents | e90a783a4e8b |
| children | 49d672730d3e |
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| 57:d3095ad12f24 | 58:d53281e6edae |
|---|---|
| 1 <tool id="merge_sites" name="4. Merge Sites" version="1.0.1" profile="16.10"> | 1 <tool id="merge_sites" name="4. Merge Sites" version="1.0.1" profile="16.10"> |
| 2 <description>from multiple samples</description> | 2 <description>from multiple samples</description> |
| 3 <requirements> | 3 <requirements> |
| 4 <requirement type="package" version="2.3.5">bowtie2</requirement> | 4 <container type="docker">quay.io/biocontainers/mulled-v2-a9689be5d4f7dc232fcd76f2f32bef2b80afcb49:0560aee94873e022862623c7766c9634a09b9513-0</container> |
| 5 <requirement type="package" version="2.4.5">bowtie2</requirement> | |
| 5 <requirement type="package" version="1.9">samtools</requirement> | 6 <requirement type="package" version="1.9">samtools</requirement> |
| 6 <requirement type="package" version="1.0.6">bzip2</requirement> | 7 <requirement type="package" version="1.0.8">bzip2</requirement> |
| 7 <requirement type="package" version="2.0.2">snp-pipeline</requirement> | 8 <requirement type="package" version="2.2.1">snp-pipeline</requirement> |
| 8 <requirement type="package" version="3.6.8">python</requirement> | 9 <!-- <requirement type="package" version="3.6.8">python</requirement> --> |
| 9 </requirements> | 10 </requirements> |
| 10 <command detect_errors="exit_code"><![CDATA[ | 11 <command detect_errors="exit_code"><![CDATA[ |
| 11 export LD_LIBRARY_PATH="\$CONDA_DEFAULT_ENV/lib" && | 12 export LD_LIBRARY_PATH="\$CONDA_DEFAULT_ENV/lib" && |
| 12 python $__tool_directory__/snp-wind.py ./ | 13 python $__tool_directory__/snp-wind.py ./ |
| 13 #for $call in $calls | 14 #for $call in $calls |
| 30 <element name="sample2" value="samples/sample2/var.flt_preserved.vcf" ftype="fastqsanger" /> | 31 <element name="sample2" value="samples/sample2/var.flt_preserved.vcf" ftype="fastqsanger" /> |
| 31 <element name="sample3" value="samples/sample3/var.flt_preserved.vcf" ftype="fastqsanger" /> | 32 <element name="sample3" value="samples/sample3/var.flt_preserved.vcf" ftype="fastqsanger" /> |
| 32 <element name="sample4" value="samples/sample4/var.flt_preserved.vcf" ftype="fastqsanger" /> | 33 <element name="sample4" value="samples/sample4/var.flt_preserved.vcf" ftype="fastqsanger" /> |
| 33 </collection> | 34 </collection> |
| 34 </param> | 35 </param> |
| 35 <!-- <output name="snplist" value="snplist.txt" /> --> | 36 <output name="snplist" value="snplist.txt" /> |
| 36 </test> | 37 </test> |
| 37 </tests> | 38 </tests> |
| 38 <help><![CDATA[ | 39 <help><![CDATA[ |
| 39 <a href="http://snp-pipeline.readthedocs.io/en/latest/index.html">http://snp-pipeline.readthedocs.io/en/latest/index.html</a> | 40 <a href="http://snp-pipeline.readthedocs.io/en/latest/index.html">http://snp-pipeline.readthedocs.io/en/latest/index.html</a> |
| 40 ]]></help> | 41 ]]></help> |