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1 <tool id="call_amr_mutations" name="PIMA: call AMR mutations" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description></description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <command detect_errors="exit_code"><![CDATA[
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8 #import os
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9
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10 #if $os.path.getsize(str($varscan_raw)) > 0:
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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 &&
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12 cat varscan_snp | awk '{OFS = "\t"; print $1,$2,".",$3,$4,-log($14),"PASS",".","GT","1|1"}' > snp_vcf &&
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13 cat snp_vcf | sort -k 1,1 -k 2n,2n | awk 'BEGIN{OFS = "\t";print "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tSAMPLE"}{print}' > '$varscan_vcf'
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14 #end if
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15 ]]></command>
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16 <inputs>
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17 <param name="varscan_raw" type="data" format="vcf" label="Raw varscan VCF file"/>
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18 <param name="mutation_regions" type="data" format="bed" label="AMR mutation regions BED file"/>
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19 </inputs>
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20 <outputs>
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21 <data name="varscan_vcf" format="vcf"/>
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22 </outputs>
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23 <tests>
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24 <test>
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25 <param name="varscan_raw" value="input1.vcf" ftype="vcf"/>
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26 <param name="mutation_regions" value="mutation_regions.bed" ftype="bed"/>
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2
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27 <output name="varscan_vcf" value="output1.vcf" ftype="vcf"/>
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28 </test>
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29 </tests>
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30 <help>
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31 **What it does**
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32
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33 Accepts VarScan mpileup2snps file, filters them, and produces a VCF file.
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34 </help>
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35 <expand macro="citations"/>
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36 </tool>
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37
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