Mercurial > repos > greg > call_amr_mutations
view call_amr_mutations.xml @ 2:a2fe87395f74 draft
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author | greg |
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date | Mon, 20 Feb 2023 21:10:42 +0000 |
parents | 52a9e19ae588 |
children | 30b17a17c1aa |
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<tool id="call_amr_mutations" name="PIMA: call AMR mutations" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> <description></description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"/> <command detect_errors="exit_code"><![CDATA[ #import os #if $os.path.getsize(str($varscan_raw)) > 0: cat '$varscan_raw' | awk '(NR > 1 && $9 == 2 && $5 + $6 >= 15){OFS = "\t";f = $6 / ($5 + $6); gsub(/.*\//, "", $4);s = $4;gsub(/[+\\-]/, "", s);$7 = sprintf("%.2f%%", f * 100);min = 1 / log(length(s) + 2) / log(10) + 2/10;if(f > min){print}}' > varscan_snp && cat varscan_snp | awk '{OFS = "\t"; print $1,$2,".",$3,$4,-log($14),"PASS",".","GT","1|1"}' > snp_vcf && cat snp_vcf | sort -k 1,1 -k 2n,2n | awk 'BEGIN{OFS = "\t";print "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tSAMPLE"}{print}' > '$varscan_vcf' #end if ]]></command> <inputs> <param name="varscan_raw" type="data" format="vcf" label="Raw varscan VCF file"/> <param name="mutation_regions" type="data" format="bed" label="AMR mutation regions BED file"/> </inputs> <outputs> <data name="varscan_vcf" format="vcf"/> </outputs> <tests> <test> <param name="varscan_raw" value="input1.vcf" ftype="vcf"/> <param name="mutation_regions" value="mutation_regions.bed" ftype="bed"/> <output name="varscan_vcf" value="output1.vcf" ftype="vcf"/> </test> </tests> <help> **What it does** Accepts VarScan mpileup2snps file, filters them, and produces a VCF file. </help> <expand macro="citations"/> </tool>