Mercurial > repos > greg > call_amr_mutations
comparison 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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1:52a9e19ae588 | 2:a2fe87395f74 |
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7 <command detect_errors="exit_code"><![CDATA[ | 7 <command detect_errors="exit_code"><![CDATA[ |
8 #import os | 8 #import os |
9 | 9 |
10 #if $os.path.getsize(str($varscan_raw)) > 0: | 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);$7 = sprintf("%.2f%%", f * 100);min = 1 / log(length(s) + 2) / log(10) + 2/10;if(f > min){print}}' > varscan_snp && | 11 cat '$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_tsv && | 12 cat varscan_snp | awk '{OFS = "\t"; print $1,$2,".",$3,$4,-log($14),"PASS",".","GT","1|1"}' > snp_vcf && |
13 cat varscan_snp_tsv | sort -k 1,1 -k 2n,2n | awk 'BEGIN{OFS = "\t";print "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tSAMPLE"}{print}' > '$varscan_tsv' | 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 | 14 #end if |
15 ]]></command> | 15 ]]></command> |
16 <inputs> | 16 <inputs> |
17 <param name="varscan_raw" type="data" format="vcf" label="Raw varscan VCF file"/> | 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"/> | 18 <param name="mutation_regions" type="data" format="bed" label="AMR mutation regions BED file"/> |
19 </inputs> | 19 </inputs> |
20 <outputs> | 20 <outputs> |
21 <data name="varscan_tsv" format="tsv"/> | 21 <data name="varscan_vcf" format="vcf"/> |
22 </outputs> | 22 </outputs> |
23 <tests> | 23 <tests> |
24 <test> | 24 <test> |
25 <param name="varscan_raw" value="input1.vcf" ftype="vcf"/> | 25 <param name="varscan_raw" value="input1.vcf" ftype="vcf"/> |
26 <param name="mutation_regions" value="mutation_regions.bed" ftype="bed"/> | 26 <param name="mutation_regions" value="mutation_regions.bed" ftype="bed"/> |
27 <output name="varscan_tsv" value="output1.tsv" ftype="tsv"/> | 27 <output name="varscan_vcf" value="output1.vcf" ftype="vcf"/> |
28 </test> | 28 </test> |
29 </tests> | 29 </tests> |
30 <help> | 30 <help> |
31 **What it does** | 31 **What it does** |
32 | 32 |