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comparison call_amr_mutations.xml @ 0:64999b5b58fe draft

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author greg
date Fri, 10 Feb 2023 17:35:04 +0000
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1 <tool id="call_amr_mutations" name="PIMA: call AMR mutations" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description></description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <command detect_errors="exit_code"><![CDATA[
8 #import os
9
10 #if $os.path.getsize(str($varscan_raw)) > 0:
11 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 &&
12 cat varscan_snp | awk '{OFS = "\t"; print $1,$2,".",$3,$4,-log($14),"PASS",".","GT","1|1"}' > varscan_snp_vcf &&
13 cat varscan_snp_vcf | sort -k 1,1 -k 2n,2n | awk 'BEGIN{OFS = "\t";print "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tSAMPLE"}{print}' > '$varscan_vcf'
14 #end if
15 ]]></command>
16 <inputs>
17 <param name="varscan_raw" type="data" format="vcf" label="Raw varscan VCF file"/>
18 <param name="mutation_regions" type="data" format="bed" label="AMR mutation regions BED file"/>
19 </inputs>
20 <outputs>
21 <data name="varscan_vcf" format="vcf"/>
22 </outputs>
23 <tests>
24 <test>
25 <param name="varscan_raw" value="varscan_raw.vcf" ftype="vcf"/>
26 <param name="mutation_regions" value="mutation_regions.bed" ftype="bed"/>
27 <output name="varscan_vcf" value="varscan_vcf.vcf" ftype="vcf"/>
28 </test>
29 </tests>
30 <help>
31 **What it does**
32
33 Accepts VarScan mpileup2snps file, filters them, and produces a VCF file.
34 </help>
35 <expand macro="citations"/>
36 </tool>
37