Mercurial > repos > greg > call_amr_mutations

comparison call_amr_mutations.xml @ 3:30b17a17c1aa draft

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author greg
date Tue, 21 Mar 2023 19:26:55 +0000
parents a2fe87395f74
children 2774bdf30122
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2:a2fe87395f74 3:30b17a17c1aa
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <command detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
8 #import os 8 ## NOTE: This tool provides the functionality of the PIMA filter_varsacn()
9 ## function here https://github.com/appliedbinf/pima_md/blob/main/pima.py#L3012
9 10
10 #if $os.path.getsize(str($varscan_raw)) > 0: 11 python '$__tool_directory__/filter_varscan.py'
11 cat '$varscan_raw' | awk '(NR > 1 && $9 == 2 && $5 + $6 >= 15){OFS = "\t";f = $6 / ($5 + $6); gsub(/.*\//, "", $4);s = $4;gsub(/[+\\-]/, "", s);$7 = sprintf("%.2f%%", f * 100);min = 1 / log(length(s) + 2) / log(10) + 2/10;if(f > min){print}}' > varscan_snp && 12 --varscan_raw '$varscan_raw'
12 cat varscan_snp | awk '{OFS = "\t"; print $1,$2,".",$3,$4,-log($14),"PASS",".","GT","1|1"}' > snp_vcf && 13 --output '$output'
13 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'
14 #end if
15 ]]></command> 14 ]]></command>
16 <inputs> 15 <inputs>
17 <param name="varscan_raw" type="data" format="vcf" label="Raw varscan VCF file"/> 16 <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> 17 </inputs>
20 <outputs> 18 <outputs>
21 <data name="varscan_vcf" format="vcf"/> 19 <data name="output" format="vcf"/>
22 </outputs> 20 </outputs>
23 <tests> 21 <tests>
24 <test> 22 <test>
25 <param name="varscan_raw" value="input1.vcf" ftype="vcf"/> 23 <param name="varscan_raw" value="input.vcf" ftype="vcf"/>
26 <param name="mutation_regions" value="mutation_regions.bed" ftype="bed"/> 24 <output name="output" value="output.vcf" ftype="vcf"/>
27 <output name="varscan_vcf" value="output1.vcf" ftype="vcf"/>
28 </test> 25 </test>
29 </tests> 26 </tests>
30 <help> 27 <help>
31 **What it does** 28 **What it does**
32 29
33 Accepts VarScan mpileup2snps file, filters them, and produces a VCF file. 30 Accepts VarScan mpileup2snps VCF file, filters it, and produces a filtered VCF file.
34 </help> 31 </help>
35 <expand macro="citations"/> 32 <expand macro="citations"/>
36 </tool> 33 </tool>
37