Mercurial > repos > greg > cfsan_snp_pipeline_merge_sites
view cfsan_snp_pipeline_merge_sites.xml @ 4:36e984464e12 draft default tip
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author | greg |
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date | Thu, 23 Nov 2023 18:59:44 +0000 |
parents | bb483baa0e50 |
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<tool id="cfsan_snp_pipeline_merge_sites" name="CFSAN SNP Pipeline: merge sites" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> <description>from multiple samples</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"/> <command detect_errors="exit_code"><![CDATA[ python '$__tool_directory__/snp_wind.py' ./ #for $input_vcf in $input_vcf_collection: -n '$input_vcf.element_identifier' -f '$input_vcf' #end for -p 'var.fit.vcf' > ./file && cfsan_snp_pipeline merge_sites -v 4 -n 'var.fit.vcf' ./file ./filtered_snps -o '$output' ]]></command> <inputs> <param name="input_vcf_collection" type="data_collection" format="vcf" collection_type="list" label="Collection of VCF files"/> </inputs> <outputs> <data name="output" format="tabular"/> </outputs> <tests> <test> <param name="input_vcf_collection"> <collection type="list"> <element name="input1" value="input1.vcf" ftype="vcf"/> <element name="input2" value="input2.vcf" ftype="vcf"/> <element name="input3" value="input3.vcf" ftype="vcf"/> <element name="input4" value="input4.vcf" ftype="vcf"/> </collection> </param> <output name="output" value="output2.tabular"/> </test> </tests> <help><![CDATA[ **What it does** Combine the SNP positions across all samples into a single unified SNP list file identifing the positions and sample names where SNPs were called. **Optional parameters** * **force** - Force processing even when result file already exists and is newer than inputs (default: False) * **vcfname** - File name of the VCF files which must exist in each of the sample directories (default: var.flt.vcf) * **maxsnps** - Exclude samples having more than this maximum allowed number of SNPs. Set to -1 to disable this function (default: -1) **More information** CFSAN SNP Pipeline `merge sites documentation <https://snp-pipeline.readthedocs.io/en/latest/cmd_ref.html#merge-sites>`_ ]]></help> <expand macro="citations"/> </tool>