diff call_amr_mutations.xml @ 2:a2fe87395f74 draft

Uploaded

--- a/call_amr_mutations.xml	Mon Feb 20 19:56:50 2023 +0000
+++ b/call_amr_mutations.xml	Mon Feb 20 21:10:42 2023 +0000
@@ -9,8 +9,8 @@
 
 #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($14),"PASS",".","GT","1|1"}' > varscan_snp_tsv &&
-    cat varscan_snp_tsv | sort -k 1,1 -k 2n,2n | awk 'BEGIN{OFS = "\t";print "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tSAMPLE"}{print}' > '$varscan_tsv'
+    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>
@@ -18,13 +18,13 @@
         <param name="mutation_regions" type="data" format="bed" label="AMR mutation regions BED file"/>
     </inputs>
     <outputs>
-        <data name="varscan_tsv" format="tsv"/>
+        <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_tsv" value="output1.tsv" ftype="tsv"/>
+            <output name="varscan_vcf" value="output1.vcf" ftype="vcf"/>
         </test>
     </tests>
     <help>