# HG changeset patch
# User greg
# Date 1676927442 0
# Node ID a2fe87395f74214e4e46bd4cd083523b3330baba
# Parent  52a9e19ae58815f4ab85aeb11ede07b6fc940400
Uploaded

diff -r 52a9e19ae588 -r a2fe87395f74 call_amr_mutations.xml
--- 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>
diff -r 52a9e19ae588 -r a2fe87395f74 test-data/output1.tsv
--- a/test-data/output1.tsv	Mon Feb 20 19:56:50 2023 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,95 +0,0 @@
-#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	SAMPLE
-chromosome	6848	.	C	T	0	PASS	.	GT	1|1
-chromosome	28975	.	G	A	0	PASS	.	GT	1|1
-chromosome	64632	.	T	C	0	PASS	.	GT	1|1
-chromosome	73738	.	T	C	0	PASS	.	GT	1|1
-chromosome	122896	.	G	A	0	PASS	.	GT	1|1
-chromosome	171823	.	C	T	0	PASS	.	GT	1|1
-chromosome	182106	.	C	T	0	PASS	.	GT	1|1
-chromosome	200731	.	C	T	0	PASS	.	GT	1|1
-chromosome	240050	.	T	C	0	PASS	.	GT	1|1
-chromosome	243867	.	C	T	0	PASS	.	GT	1|1
-chromosome	245190	.	C	T	0	PASS	.	GT	1|1
-chromosome	274236	.	C	A	0	PASS	.	GT	1|1
-chromosome	318187	.	C	T	0	PASS	.	GT	1|1
-chromosome	337241	.	T	C	0	PASS	.	GT	1|1
-chromosome	359536	.	G	A	0	PASS	.	GT	1|1
-chromosome	387637	.	G	A	0	PASS	.	GT	1|1
-chromosome	433277	.	G	T	0	PASS	.	GT	1|1
-chromosome	513052	.	C	T	0	PASS	.	GT	1|1
-chromosome	521963	.	A	G	0	PASS	.	GT	1|1
-chromosome	571199	.	G	A	0	PASS	.	GT	1|1
-chromosome	644625	.	T	C	0	PASS	.	GT	1|1
-chromosome	665308	.	T	C	0	PASS	.	GT	1|1
-chromosome	692932	.	C	T	0	PASS	.	GT	1|1
-chromosome	702761	.	G	C	0	PASS	.	GT	1|1
-chromosome	732173	.	A	T	0	PASS	.	GT	1|1
-chromosome	765499	.	A	C	0	PASS	.	GT	1|1
-chromosome	789298	.	G	A	0	PASS	.	GT	1|1
-chromosome	814684	.	T	G	0	PASS	.	GT	1|1
-chromosome	1023150	.	A	G	0	PASS	.	GT	1|1
-chromosome	1120096	.	C	T	0	PASS	.	GT	1|1
-chromosome	1131906	.	T	C	0	PASS	.	GT	1|1
-chromosome	1181950	.	A	G	0	PASS	.	GT	1|1
-chromosome	1184347	.	G	A	0	PASS	.	GT	1|1
-chromosome	1223198	.	C	T	0	PASS	.	GT	1|1
-chromosome	1270555	.	G	T	0	PASS	.	GT	1|1
-chromosome	1306861	.	C	T	0	PASS	.	GT	1|1
-chromosome	1385721	.	G	A	0	PASS	.	GT	1|1
-chromosome	1406212	.	C	T	0	PASS	.	GT	1|1
-chromosome	1423420	.	A	G	0	PASS	.	GT	1|1
-chromosome	1592398	.	C	A	0	PASS	.	GT	1|1
-chromosome	1621512	.	C	A	0	PASS	.	GT	1|1
-chromosome	1631941	.	G	T	0	PASS	.	GT	1|1
-chromosome	1728049	.	G	A	0	PASS	.	GT	1|1
-chromosome	1774177	.	C	T	0	PASS	.	GT	1|1
-chromosome	1797708	.	T	C	0	PASS	.	GT	1|1
-chromosome	1798769	.	G	T	0	PASS	.	GT	1|1
-chromosome	1867996	.	T	C	0	PASS	.	GT	1|1
-chromosome	1982986	.	C	T	0	PASS	.	GT	1|1
-chromosome	2067935	.	G	A	0	PASS	.	GT	1|1
-chromosome	2133680	.	G	T	0	PASS	.	GT	1|1
-chromosome	2371243	.	T	C	0	PASS	.	GT	1|1
-chromosome	2423657	.	A	G	0	PASS	.	GT	1|1
-chromosome	2749671	.	A	G	0	PASS	.	GT	1|1
-chromosome	2834318	.	G	A	0	PASS	.	GT	1|1
-chromosome	2956135	.	G	A	0	PASS	.	GT	1|1
-chromosome	2989856	.	G	A	0	PASS	.	GT	1|1
-chromosome	3038888	.	T	C	0	PASS	.	GT	1|1
-chromosome	3163858	.	A	G	0	PASS	.	GT	1|1
-chromosome	3306423	.	C	T	0	PASS	.	GT	1|1
-chromosome	3364887	.	G	A	0	PASS	.	GT	1|1
-chromosome	3382079	.	C	T	0	PASS	.	GT	1|1
-chromosome	3460779	.	T	C	0	PASS	.	GT	1|1
-chromosome	3568849	.	A	G	0	PASS	.	GT	1|1
-chromosome	3696168	.	C	T	0	PASS	.	GT	1|1
-chromosome	3712048	.	T	C	0	PASS	.	GT	1|1
-chromosome	3739850	.	A	G	0	PASS	.	GT	1|1
-chromosome	3758015	.	A	G	0	PASS	.	GT	1|1
-chromosome	3841816	.	G	A	0	PASS	.	GT	1|1
-chromosome	4035203	.	T	C	0	PASS	.	GT	1|1
-chromosome	4145299	.	C	T	0	PASS	.	GT	1|1
-chromosome	4147376	.	C	T	0	PASS	.	GT	1|1
-chromosome	4158968	.	C	T	0	PASS	.	GT	1|1
-chromosome	4212929	.	G	T	0	PASS	.	GT	1|1
-chromosome	4232753	.	C	T	0	PASS	.	GT	1|1
-chromosome	4345557	.	T	A	0	PASS	.	GT	1|1
-chromosome	4456896	.	G	A	0	PASS	.	GT	1|1
-chromosome	4501001	.	G	A	0	PASS	.	GT	1|1
-chromosome	4519053	.	A	G	0	PASS	.	GT	1|1
-chromosome	4519433	.	C	A	0	PASS	.	GT	1|1
-chromosome	4698084	.	T	C	0	PASS	.	GT	1|1
-chromosome	4929312	.	T	G	0	PASS	.	GT	1|1
-chromosome	4951610	.	G	A	0	PASS	.	GT	1|1
-chromosome	5040523	.	C	T	0	PASS	.	GT	1|1
-chromosome	5077771	.	G	A	0	PASS	.	GT	1|1
-chromosome	5140491	.	G	A	0	PASS	.	GT	1|1
-chromosome	5157810	.	G	A	0	PASS	.	GT	1|1
-pXO1	7452	.	C	T	0	PASS	.	GT	1|1
-pXO1	28077	.	G	A	0	PASS	.	GT	1|1
-pXO1	55874	.	A	T	0	PASS	.	GT	1|1
-pXO1	77518	.	A	G	0	PASS	.	GT	1|1
-pXO1	141921	.	T	G	0	PASS	.	GT	1|1
-pXO1	141922	.	T	A	0	PASS	.	GT	1|1
-pXO1	141923	.	T	A	0	PASS	.	GT	1|1
-pXO1	150892	.	C	A	0	PASS	.	GT	1|1
diff -r 52a9e19ae588 -r a2fe87395f74 test-data/output1.vcf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output1.vcf	Mon Feb 20 21:10:42 2023 +0000
@@ -0,0 +1,95 @@
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	SAMPLE
+chromosome	6848	.	C	T	0	PASS	.	GT	1|1
+chromosome	28975	.	G	A	0	PASS	.	GT	1|1
+chromosome	64632	.	T	C	0	PASS	.	GT	1|1
+chromosome	73738	.	T	C	0	PASS	.	GT	1|1
+chromosome	122896	.	G	A	0	PASS	.	GT	1|1
+chromosome	171823	.	C	T	0	PASS	.	GT	1|1
+chromosome	182106	.	C	T	0	PASS	.	GT	1|1
+chromosome	200731	.	C	T	0	PASS	.	GT	1|1
+chromosome	240050	.	T	C	0	PASS	.	GT	1|1
+chromosome	243867	.	C	T	0	PASS	.	GT	1|1
+chromosome	245190	.	C	T	0	PASS	.	GT	1|1
+chromosome	274236	.	C	A	0	PASS	.	GT	1|1
+chromosome	318187	.	C	T	0	PASS	.	GT	1|1
+chromosome	337241	.	T	C	0	PASS	.	GT	1|1
+chromosome	359536	.	G	A	0	PASS	.	GT	1|1
+chromosome	387637	.	G	A	0	PASS	.	GT	1|1
+chromosome	433277	.	G	T	0	PASS	.	GT	1|1
+chromosome	513052	.	C	T	0	PASS	.	GT	1|1
+chromosome	521963	.	A	G	0	PASS	.	GT	1|1
+chromosome	571199	.	G	A	0	PASS	.	GT	1|1
+chromosome	644625	.	T	C	0	PASS	.	GT	1|1
+chromosome	665308	.	T	C	0	PASS	.	GT	1|1
+chromosome	692932	.	C	T	0	PASS	.	GT	1|1
+chromosome	702761	.	G	C	0	PASS	.	GT	1|1
+chromosome	732173	.	A	T	0	PASS	.	GT	1|1
+chromosome	765499	.	A	C	0	PASS	.	GT	1|1
+chromosome	789298	.	G	A	0	PASS	.	GT	1|1
+chromosome	814684	.	T	G	0	PASS	.	GT	1|1
+chromosome	1023150	.	A	G	0	PASS	.	GT	1|1
+chromosome	1120096	.	C	T	0	PASS	.	GT	1|1
+chromosome	1131906	.	T	C	0	PASS	.	GT	1|1
+chromosome	1181950	.	A	G	0	PASS	.	GT	1|1
+chromosome	1184347	.	G	A	0	PASS	.	GT	1|1
+chromosome	1223198	.	C	T	0	PASS	.	GT	1|1
+chromosome	1270555	.	G	T	0	PASS	.	GT	1|1
+chromosome	1306861	.	C	T	0	PASS	.	GT	1|1
+chromosome	1385721	.	G	A	0	PASS	.	GT	1|1
+chromosome	1406212	.	C	T	0	PASS	.	GT	1|1
+chromosome	1423420	.	A	G	0	PASS	.	GT	1|1
+chromosome	1592398	.	C	A	0	PASS	.	GT	1|1
+chromosome	1621512	.	C	A	0	PASS	.	GT	1|1
+chromosome	1631941	.	G	T	0	PASS	.	GT	1|1
+chromosome	1728049	.	G	A	0	PASS	.	GT	1|1
+chromosome	1774177	.	C	T	0	PASS	.	GT	1|1
+chromosome	1797708	.	T	C	0	PASS	.	GT	1|1
+chromosome	1798769	.	G	T	0	PASS	.	GT	1|1
+chromosome	1867996	.	T	C	0	PASS	.	GT	1|1
+chromosome	1982986	.	C	T	0	PASS	.	GT	1|1
+chromosome	2067935	.	G	A	0	PASS	.	GT	1|1
+chromosome	2133680	.	G	T	0	PASS	.	GT	1|1
+chromosome	2371243	.	T	C	0	PASS	.	GT	1|1
+chromosome	2423657	.	A	G	0	PASS	.	GT	1|1
+chromosome	2749671	.	A	G	0	PASS	.	GT	1|1
+chromosome	2834318	.	G	A	0	PASS	.	GT	1|1
+chromosome	2956135	.	G	A	0	PASS	.	GT	1|1
+chromosome	2989856	.	G	A	0	PASS	.	GT	1|1
+chromosome	3038888	.	T	C	0	PASS	.	GT	1|1
+chromosome	3163858	.	A	G	0	PASS	.	GT	1|1
+chromosome	3306423	.	C	T	0	PASS	.	GT	1|1
+chromosome	3364887	.	G	A	0	PASS	.	GT	1|1
+chromosome	3382079	.	C	T	0	PASS	.	GT	1|1
+chromosome	3460779	.	T	C	0	PASS	.	GT	1|1
+chromosome	3568849	.	A	G	0	PASS	.	GT	1|1
+chromosome	3696168	.	C	T	0	PASS	.	GT	1|1
+chromosome	3712048	.	T	C	0	PASS	.	GT	1|1
+chromosome	3739850	.	A	G	0	PASS	.	GT	1|1
+chromosome	3758015	.	A	G	0	PASS	.	GT	1|1
+chromosome	3841816	.	G	A	0	PASS	.	GT	1|1
+chromosome	4035203	.	T	C	0	PASS	.	GT	1|1
+chromosome	4145299	.	C	T	0	PASS	.	GT	1|1
+chromosome	4147376	.	C	T	0	PASS	.	GT	1|1
+chromosome	4158968	.	C	T	0	PASS	.	GT	1|1
+chromosome	4212929	.	G	T	0	PASS	.	GT	1|1
+chromosome	4232753	.	C	T	0	PASS	.	GT	1|1
+chromosome	4345557	.	T	A	0	PASS	.	GT	1|1
+chromosome	4456896	.	G	A	0	PASS	.	GT	1|1
+chromosome	4501001	.	G	A	0	PASS	.	GT	1|1
+chromosome	4519053	.	A	G	0	PASS	.	GT	1|1
+chromosome	4519433	.	C	A	0	PASS	.	GT	1|1
+chromosome	4698084	.	T	C	0	PASS	.	GT	1|1
+chromosome	4929312	.	T	G	0	PASS	.	GT	1|1
+chromosome	4951610	.	G	A	0	PASS	.	GT	1|1
+chromosome	5040523	.	C	T	0	PASS	.	GT	1|1
+chromosome	5077771	.	G	A	0	PASS	.	GT	1|1
+chromosome	5140491	.	G	A	0	PASS	.	GT	1|1
+chromosome	5157810	.	G	A	0	PASS	.	GT	1|1
+pXO1	7452	.	C	T	0	PASS	.	GT	1|1
+pXO1	28077	.	G	A	0	PASS	.	GT	1|1
+pXO1	55874	.	A	T	0	PASS	.	GT	1|1
+pXO1	77518	.	A	G	0	PASS	.	GT	1|1
+pXO1	141921	.	T	G	0	PASS	.	GT	1|1
+pXO1	141922	.	T	A	0	PASS	.	GT	1|1
+pXO1	141923	.	T	A	0	PASS	.	GT	1|1
+pXO1	150892	.	C	A	0	PASS	.	GT	1|1