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author | greg |
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date | Thu, 12 Oct 2023 19:55:24 +0000 |
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children | bbf17f071638 |
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<tool id="cfsan_snp_pipeline_filter_snp_regions" name="CFSAN SNP Pipeline: filter SNP Regions" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> <description>based on location</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"/> <command detect_errors="exit_code"><![CDATA[ #if str($reference_cond.reference_source) == 'cached' #set reference = $reference_cond.reference.fields.path #else: #set reference = $reference_cond.reference #end if mkdir -p ./samples/sample/ && ln -s '$calls' ./samples/sample/var.flt.vcf && echo "\$PWD/samples/sample" > ./alignment.txt && cfsan_snp_pipeline filter_regions ./alignment.txt '$reference' && cp ./samples/sample/var.flt_preserved.vcf '$filcalls' && cp ./samples/sample/var.flt_removed.vcf '$excludes' ]]></command> <inputs> <param name="calls" type="data" format="vcf" label="Unfiltered SNP calls from your history"/> <expand macro="reference_cond"/> </inputs> <outputs> <data name="filcalls" format="vcf" label="Filtered SNPs"/> <data name="excludes" format="vcf" label="SNPs excluded by filtering"/> </outputs> <tests> <test> <param name="calls" value="input.vcf" /> <param name="reference_source" value="history"/> <param name="reference" value="lambda_virus.fasta"/> <output name="filcalls" value="output_preserved.vcf" lines_diff="6"/> <output name="excludes" value="output_removed.vcf" lines_diff="6"/> </test> </tests> <help><![CDATA[ **What it does** Remove abnormally dense SNPs from the input VCF file, save the reserved SNPs into a new VCF file, and save the removed SNPs into another VCF file. **Optional parameters** * **force** - Force processing even when result files already exist and are newer than inputs (default: False) * **vcfname** - File name of the input VCF files which must exist in each of the sample directories (default: var.flt.vcf) * **edge_length** - The length of the edge regions in a contig, in which all SNPs will be removed. (default: 500) * **window_size** - The length of the window in which the number of SNPs should be no more than max_num_snp. (default: [1000]) * **max_snp** - The maximum number of SNPs allowed in a window. (default: [3]) * **out_group** - Relative or absolute path to the file indicating outgroup samples, one sample ID per line. (default: None) **More information** [CFSAN SNP Pipeline documentation](http://snp-pipeline.readthedocs.io/en/latest/index.html">http://snp-pipeline.readthedocs.io/en/latest/index.html) ]]></help> <expand macro="citations"/> </tool>