# HG changeset patch
# User blankenberg
# Date 1522767131 14400
# Node ID 07e71cf6c8ef40720ec2a9c6b7630029e4980061
# Parent  aff38ea879f1969fa1c514189323de8e494ca2e0
planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/naive_variant_caller commit 56487ac8b5d91755e44d4e326105cdb9e409a66c

diff -r aff38ea879f1 -r 07e71cf6c8ef naive_variant_caller.xml
--- a/naive_variant_caller.xml	Wed Feb 28 16:01:52 2018 -0500
+++ b/naive_variant_caller.xml	Tue Apr 03 10:52:11 2018 -0400
@@ -1,7 +1,7 @@
-<tool id="naive_variant_caller" name="Naive Variant Caller (NVC)" version="0.0.3">
+<tool id="naive_variant_caller" name="Naive Variant Caller (NVC)" version="0.0.4">
   <description> - tabulate variable sites from BAM datasets</description>
   <requirements>
-    <requirement type="package" version="0.0.3">nvc</requirement>
+    <requirement type="package" version="0.0.4">nvc</requirement>
   </requirements>
   <stdio>
     <exit_code range="1:" />
@@ -103,7 +103,7 @@
     <param name="ploidy" type="integer" value="2" min="1" label="Ploidy" />
     <param name="variants_only" type="boolean" truevalue="--variants_only" falsevalue="" checked="False" label="Only write out positions with possible alternate alleles"/>
     
-    <param name="use_strand" type="boolean" truevalue="--use_strand" falsevalue="" checked="False" label="Report counts by strand"/>
+    <param name="use_strand" type="boolean" truevalue="--use_strand" falsevalue="" checked="True" label="Report counts by strand"/>
     
     <conditional name="advanced_options">
         <param name="advanced_options_selector" type="select" label="Show Advanced Options">
@@ -145,6 +145,21 @@
           <param name="coverage_dtype" value="uint8" />
           <output name="output_vcf" file="fake_phiX174_reads_1_test_out_1.vcf" compare="contains" />
       </test>
+      <test>
+          <param name="reference_source_selector" value="history" />
+          <param name="input_bam" value="fake_phiX174_reads_1.bam" ftype="bam" />
+          <param name="ref_file" value="phiX174.fasta" ftype="fasta" />
+          <param name="regions" value="0" />
+          <param name="min_support_depth" value="0" />
+          <param name="min_base_quality" value="" />
+          <param name="min_mapping_quality" value="" />
+          <param name="ploidy" value="2" />
+          <param name="variants_only" value="False" />
+          <param name="use_strand" value="True" />
+          <param name="advanced_options_selector" value="advanced" />
+          <param name="coverage_dtype" value="uint8" />
+          <output name="output_vcf" file="fake_phiX174_reads_1_test_out_2.vcf" compare="contains" />
+      </test>
   </tests>
   <help>
 The **Naive Variant Caller** tool (NVC).
diff -r aff38ea879f1 -r 07e71cf6c8ef test-data/fake_phiX174_reads_1_test_out_1.vcf
--- a/test-data/fake_phiX174_reads_1_test_out_1.vcf	Wed Feb 28 16:01:52 2018 -0500
+++ b/test-data/fake_phiX174_reads_1_test_out_1.vcf	Tue Apr 03 10:52:11 2018 -0400
@@ -1,4 +1,5 @@
-##fileformat=VCFv4.1
+##fileformat=VCFv4.3
+##source=Naive Variant Caller version 0.0.4
 ##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
 ##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
@@ -6,46 +7,46 @@
 ##FORMAT=<ID=AF,Number=.,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
 ##FORMAT=<ID=NC,Number=.,Type=String,Description="Nucleotide and indel counts">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	A Fake phiX Sample
-phiX174	1411	.	A	.	.	.	AC=;AF=	GT:AC:AF:NC	0/0:::A=1,
-phiX174	1412	.	G	.	.	.	AC=;AF=	GT:AC:AF:NC	0/0:::G=3,
-phiX174	1413	.	C	.	.	.	AC=;AF=	GT:AC:AF:NC	0/0:::C=5,
-phiX174	1414	.	G	.	.	.	AC=;AF=	GT:AC:AF:NC	0/0:::G=6,
-phiX174	1415	.	C	.	.	.	AC=;AF=	GT:AC:AF:NC	0/0:::C=7,
-phiX174	1416	.	C	.	.	.	AC=;AF=	GT:AC:AF:NC	0/0:::C=8,
-phiX174	1417	.	G	.	.	.	AC=;AF=	GT:AC:AF:NC	0/0:::G=9,
-phiX174	1418	.	T	.	.	.	AC=;AF=	GT:AC:AF:NC	0/0:::T=10,
-phiX174	1419	.	G	.	.	.	AC=;AF=	GT:AC:AF:NC	0/0:::G=10,
-phiX174	1420	.	G	.	.	.	AC=;AF=	GT:AC:AF:NC	0/0:::G=10,
-phiX174	1421	.	A	.	.	.	AC=;AF=	GT:AC:AF:NC	0/0:::A=10,
-phiX174	1422	.	T	.	.	.	AC=;AF=	GT:AC:AF:NC	0/0:::T=10,
-phiX174	1423	.	G	.	.	.	AC=;AF=	GT:AC:AF:NC	0/0:::G=10,
+phiX174	1411	.	A	.	.	.	AC=.;AF=.	GT:AC:AF:NC	0/0:.:.:A=1,
+phiX174	1412	.	G	.	.	.	AC=.;AF=.	GT:AC:AF:NC	0/0:.:.:G=3,
+phiX174	1413	.	C	.	.	.	AC=.;AF=.	GT:AC:AF:NC	0/0:.:.:C=5,
+phiX174	1414	.	G	.	.	.	AC=.;AF=.	GT:AC:AF:NC	0/0:.:.:G=6,
+phiX174	1415	.	C	.	.	.	AC=.;AF=.	GT:AC:AF:NC	0/0:.:.:C=7,
+phiX174	1416	.	C	.	.	.	AC=.;AF=.	GT:AC:AF:NC	0/0:.:.:C=8,
+phiX174	1417	.	G	.	.	.	AC=.;AF=.	GT:AC:AF:NC	0/0:.:.:G=9,
+phiX174	1418	.	T	.	.	.	AC=.;AF=.	GT:AC:AF:NC	0/0:.:.:T=10,
+phiX174	1419	.	G	.	.	.	AC=.;AF=.	GT:AC:AF:NC	0/0:.:.:G=10,
+phiX174	1420	.	G	.	.	.	AC=.;AF=.	GT:AC:AF:NC	0/0:.:.:G=10,
+phiX174	1421	.	A	.	.	.	AC=.;AF=.	GT:AC:AF:NC	0/0:.:.:A=10,
+phiX174	1422	.	T	.	.	.	AC=.;AF=.	GT:AC:AF:NC	0/0:.:.:T=10,
+phiX174	1423	.	G	.	.	.	AC=.;AF=.	GT:AC:AF:NC	0/0:.:.:G=10,
 phiX174	1424	.	C	A	.	.	AC=7;AF=0.7	GT:AC:AF:NC	1/0:7:0.7:A=7,C=3,
-phiX174	1425	.	C	.	.	.	AC=;AF=	GT:AC:AF:NC	0/0:::C=10,
-phiX174	1426	.	T	.	.	.	AC=;AF=	GT:AC:AF:NC	0/0:::T=10,
-phiX174	1427	.	G	.	.	.	AC=;AF=	GT:AC:AF:NC	0/0:::G=10,
-phiX174	1428	.	A	.	.	.	AC=;AF=	GT:AC:AF:NC	0/0:::A=10,
-phiX174	1429	.	C	.	.	.	AC=;AF=	GT:AC:AF:NC	0/0:::C=10,
-phiX174	1430	.	C	.	.	.	AC=;AF=	GT:AC:AF:NC	0/0:::C=10,
-phiX174	1431	.	G	.	.	.	AC=;AF=	GT:AC:AF:NC	0/0:::G=10,
-phiX174	1432	.	T	.	.	.	AC=;AF=	GT:AC:AF:NC	0/0:::T=10,
-phiX174	1433	.	A	.	.	.	AC=;AF=	GT:AC:AF:NC	0/0:::A=10,
-phiX174	1434	.	C	.	.	.	AC=;AF=	GT:AC:AF:NC	0/0:::C=10,
-phiX174	1435	.	C	.	.	.	AC=;AF=	GT:AC:AF:NC	0/0:::C=10,
-phiX174	1436	.	G	.	.	.	AC=;AF=	GT:AC:AF:NC	0/0:::G=10,
-phiX174	1437	.	A	.	.	.	AC=;AF=	GT:AC:AF:NC	0/0:::A=10,
-phiX174	1438	.	G	.	.	.	AC=;AF=	GT:AC:AF:NC	0/0:::G=10,
-phiX174	1439	.	G	.	.	.	AC=;AF=	GT:AC:AF:NC	0/0:::G=10,
-phiX174	1440	.	C	.	.	.	AC=;AF=	GT:AC:AF:NC	0/0:::C=10,
-phiX174	1441	.	T	.	.	.	AC=;AF=	GT:AC:AF:NC	0/0:::T=10,
-phiX174	1442	.	A	.	.	.	AC=;AF=	GT:AC:AF:NC	0/0:::A=10,
-phiX174	1443	.	A	.	.	.	AC=;AF=	GT:AC:AF:NC	0/0:::A=10,
-phiX174	1444	.	C	.	.	.	AC=;AF=	GT:AC:AF:NC	0/0:::C=10,
-phiX174	1445	.	C	.	.	.	AC=;AF=	GT:AC:AF:NC	0/0:::C=10,
+phiX174	1425	.	C	.	.	.	AC=.;AF=.	GT:AC:AF:NC	0/0:.:.:C=10,
+phiX174	1426	.	T	.	.	.	AC=.;AF=.	GT:AC:AF:NC	0/0:.:.:T=10,
+phiX174	1427	.	G	.	.	.	AC=.;AF=.	GT:AC:AF:NC	0/0:.:.:G=10,
+phiX174	1428	.	A	.	.	.	AC=.;AF=.	GT:AC:AF:NC	0/0:.:.:A=10,
+phiX174	1429	.	C	.	.	.	AC=.;AF=.	GT:AC:AF:NC	0/0:.:.:C=10,
+phiX174	1430	.	C	.	.	.	AC=.;AF=.	GT:AC:AF:NC	0/0:.:.:C=10,
+phiX174	1431	.	G	.	.	.	AC=.;AF=.	GT:AC:AF:NC	0/0:.:.:G=10,
+phiX174	1432	.	T	.	.	.	AC=.;AF=.	GT:AC:AF:NC	0/0:.:.:T=10,
+phiX174	1433	.	A	.	.	.	AC=.;AF=.	GT:AC:AF:NC	0/0:.:.:A=10,
+phiX174	1434	.	C	.	.	.	AC=.;AF=.	GT:AC:AF:NC	0/0:.:.:C=10,
+phiX174	1435	.	C	.	.	.	AC=.;AF=.	GT:AC:AF:NC	0/0:.:.:C=10,
+phiX174	1436	.	G	.	.	.	AC=.;AF=.	GT:AC:AF:NC	0/0:.:.:G=10,
+phiX174	1437	.	A	.	.	.	AC=.;AF=.	GT:AC:AF:NC	0/0:.:.:A=10,
+phiX174	1438	.	G	.	.	.	AC=.;AF=.	GT:AC:AF:NC	0/0:.:.:G=10,
+phiX174	1439	.	G	.	.	.	AC=.;AF=.	GT:AC:AF:NC	0/0:.:.:G=10,
+phiX174	1440	.	C	.	.	.	AC=.;AF=.	GT:AC:AF:NC	0/0:.:.:C=10,
+phiX174	1441	.	T	.	.	.	AC=.;AF=.	GT:AC:AF:NC	0/0:.:.:T=10,
+phiX174	1442	.	A	.	.	.	AC=.;AF=.	GT:AC:AF:NC	0/0:.:.:A=10,
+phiX174	1443	.	A	.	.	.	AC=.;AF=.	GT:AC:AF:NC	0/0:.:.:A=10,
+phiX174	1444	.	C	.	.	.	AC=.;AF=.	GT:AC:AF:NC	0/0:.:.:C=10,
+phiX174	1445	.	C	.	.	.	AC=.;AF=.	GT:AC:AF:NC	0/0:.:.:C=10,
 phiX174	1446	.	C	T	.	.	AC=3;AF=0.3	GT:AC:AF:NC	0/1:3:0.3:C=7,T=3,
 phiX174	1447	.	T	A	.	.	AC=2;AF=0.222222222222	GT:AC:AF:NC	0/0:2:0.222222222222:A=2,T=7,
-phiX174	1448	.	A	.	.	.	AC=;AF=	GT:AC:AF:NC	0/0:::A=7,
-phiX174	1449	.	A	.	.	.	AC=;AF=	GT:AC:AF:NC	0/0:::A=5,
-phiX174	1450	.	T	.	.	.	AC=;AF=	GT:AC:AF:NC	0/0:::T=4,
-phiX174	1451	.	G	.	.	.	AC=;AF=	GT:AC:AF:NC	0/0:::G=3,
-phiX174	1452	.	A	.	.	.	AC=;AF=	GT:AC:AF:NC	0/0:::A=2,
-phiX174	1453	.	G	.	.	.	AC=;AF=	GT:AC:AF:NC	0/0:::G=1,
+phiX174	1448	.	A	.	.	.	AC=.;AF=.	GT:AC:AF:NC	0/0:.:.:A=7,
+phiX174	1449	.	A	.	.	.	AC=.;AF=.	GT:AC:AF:NC	0/0:.:.:A=5,
+phiX174	1450	.	T	.	.	.	AC=.;AF=.	GT:AC:AF:NC	0/0:.:.:T=4,
+phiX174	1451	.	G	.	.	.	AC=.;AF=.	GT:AC:AF:NC	0/0:.:.:G=3,
+phiX174	1452	.	A	.	.	.	AC=.;AF=.	GT:AC:AF:NC	0/0:.:.:A=2,
+phiX174	1453	.	G	.	.	.	AC=.;AF=.	GT:AC:AF:NC	0/0:.:.:G=1,
diff -r aff38ea879f1 -r 07e71cf6c8ef test-data/fake_phiX174_reads_1_test_out_2.vcf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fake_phiX174_reads_1_test_out_2.vcf	Tue Apr 03 10:52:11 2018 -0400
@@ -0,0 +1,54 @@
+##fileformat=VCFv4.3
+##source=Naive Variant Caller version 0.0.4
+##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
+##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
+##INFO=<ID=SB,Number=1,Type=Float,Description="Strand Bias">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=AC,Number=.,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
+##FORMAT=<ID=AF,Number=.,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
+##FORMAT=<ID=SB,Number=1,Type=Float,Description="Strand Bias">
+##FORMAT=<ID=NC,Number=.,Type=String,Description="Nucleotide and indel counts">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	A Fake phiX Sample
+phiX174	1411	.	A	.	.	.	AC=.;AF=.;SB=0.0	GT:AC:AF:SB:NC	0/0:.:.:0.0:+A=1,
+phiX174	1412	.	G	.	.	.	AC=.;AF=.;SB=0.0	GT:AC:AF:SB:NC	0/0:.:.:0.0:+G=3,
+phiX174	1413	.	C	.	.	.	AC=.;AF=.;SB=0.0	GT:AC:AF:SB:NC	0/0:.:.:0.0:+C=5,
+phiX174	1414	.	G	.	.	.	AC=.;AF=.;SB=0.0	GT:AC:AF:SB:NC	0/0:.:.:0.0:+G=6,
+phiX174	1415	.	C	.	.	.	AC=.;AF=.;SB=0.0	GT:AC:AF:SB:NC	0/0:.:.:0.0:+C=7,
+phiX174	1416	.	C	.	.	.	AC=.;AF=.;SB=0.0	GT:AC:AF:SB:NC	0/0:.:.:0.0:+C=8,
+phiX174	1417	.	G	.	.	.	AC=.;AF=.;SB=0.0	GT:AC:AF:SB:NC	0/0:.:.:0.0:+G=9,
+phiX174	1418	.	T	.	.	.	AC=.;AF=.;SB=0.0	GT:AC:AF:SB:NC	0/0:.:.:0.0:+T=10,
+phiX174	1419	.	G	.	.	.	AC=.;AF=.;SB=0.0	GT:AC:AF:SB:NC	0/0:.:.:0.0:+G=10,
+phiX174	1420	.	G	.	.	.	AC=.;AF=.;SB=0.0	GT:AC:AF:SB:NC	0/0:.:.:0.0:+G=10,
+phiX174	1421	.	A	.	.	.	AC=.;AF=.;SB=0.0	GT:AC:AF:SB:NC	0/0:.:.:0.0:+A=10,
+phiX174	1422	.	T	.	.	.	AC=.;AF=.;SB=0.0	GT:AC:AF:SB:NC	0/0:.:.:0.0:+T=10,
+phiX174	1423	.	G	.	.	.	AC=.;AF=.;SB=0.0	GT:AC:AF:SB:NC	0/0:.:.:0.0:+G=10,
+phiX174	1424	.	C	A	.	.	AC=7;AF=0.7;SB=+Inf	GT:AC:AF:SB:NC	1/0:7:0.7:+Inf:+A=7,+C=3,
+phiX174	1425	.	C	.	.	.	AC=.;AF=.;SB=0.0	GT:AC:AF:SB:NC	0/0:.:.:0.0:+C=10,
+phiX174	1426	.	T	.	.	.	AC=.;AF=.;SB=0.0	GT:AC:AF:SB:NC	0/0:.:.:0.0:+T=10,
+phiX174	1427	.	G	.	.	.	AC=.;AF=.;SB=0.0	GT:AC:AF:SB:NC	0/0:.:.:0.0:+G=10,
+phiX174	1428	.	A	.	.	.	AC=.;AF=.;SB=0.0	GT:AC:AF:SB:NC	0/0:.:.:0.0:+A=10,
+phiX174	1429	.	C	.	.	.	AC=.;AF=.;SB=0.0	GT:AC:AF:SB:NC	0/0:.:.:0.0:+C=10,
+phiX174	1430	.	C	.	.	.	AC=.;AF=.;SB=0.0	GT:AC:AF:SB:NC	0/0:.:.:0.0:+C=10,
+phiX174	1431	.	G	.	.	.	AC=.;AF=.;SB=0.0	GT:AC:AF:SB:NC	0/0:.:.:0.0:+G=10,
+phiX174	1432	.	T	.	.	.	AC=.;AF=.;SB=0.0	GT:AC:AF:SB:NC	0/0:.:.:0.0:+T=10,
+phiX174	1433	.	A	.	.	.	AC=.;AF=.;SB=0.0	GT:AC:AF:SB:NC	0/0:.:.:0.0:+A=10,
+phiX174	1434	.	C	.	.	.	AC=.;AF=.;SB=0.0	GT:AC:AF:SB:NC	0/0:.:.:0.0:+C=10,
+phiX174	1435	.	C	.	.	.	AC=.;AF=.;SB=0.0	GT:AC:AF:SB:NC	0/0:.:.:0.0:+C=10,
+phiX174	1436	.	G	.	.	.	AC=.;AF=.;SB=0.0	GT:AC:AF:SB:NC	0/0:.:.:0.0:+G=10,
+phiX174	1437	.	A	.	.	.	AC=.;AF=.;SB=0.0	GT:AC:AF:SB:NC	0/0:.:.:0.0:+A=10,
+phiX174	1438	.	G	.	.	.	AC=.;AF=.;SB=0.0	GT:AC:AF:SB:NC	0/0:.:.:0.0:+G=10,
+phiX174	1439	.	G	.	.	.	AC=.;AF=.;SB=0.0	GT:AC:AF:SB:NC	0/0:.:.:0.0:+G=10,
+phiX174	1440	.	C	.	.	.	AC=.;AF=.;SB=0.0	GT:AC:AF:SB:NC	0/0:.:.:0.0:+C=10,
+phiX174	1441	.	T	.	.	.	AC=.;AF=.;SB=0.0	GT:AC:AF:SB:NC	0/0:.:.:0.0:+T=10,
+phiX174	1442	.	A	.	.	.	AC=.;AF=.;SB=0.0	GT:AC:AF:SB:NC	0/0:.:.:0.0:+A=10,
+phiX174	1443	.	A	.	.	.	AC=.;AF=.;SB=0.0	GT:AC:AF:SB:NC	0/0:.:.:0.0:+A=10,
+phiX174	1444	.	C	.	.	.	AC=.;AF=.;SB=0.0	GT:AC:AF:SB:NC	0/0:.:.:0.0:+C=10,
+phiX174	1445	.	C	.	.	.	AC=.;AF=.;SB=0.0	GT:AC:AF:SB:NC	0/0:.:.:0.0:+C=10,
+phiX174	1446	.	C	T	.	.	AC=3;AF=0.3;SB=+Inf	GT:AC:AF:SB:NC	0/1:3:0.3:+Inf:+C=7,+T=3,
+phiX174	1447	.	T	A	.	.	AC=2;AF=0.222222222222;SB=+Inf	GT:AC:AF:SB:NC	0/0:2:0.222222222222:+Inf:+A=2,+T=7,
+phiX174	1448	.	A	.	.	.	AC=.;AF=.;SB=0.0	GT:AC:AF:SB:NC	0/0:.:.:0.0:+A=7,
+phiX174	1449	.	A	.	.	.	AC=.;AF=.;SB=0.0	GT:AC:AF:SB:NC	0/0:.:.:0.0:+A=5,
+phiX174	1450	.	T	.	.	.	AC=.;AF=.;SB=0.0	GT:AC:AF:SB:NC	0/0:.:.:0.0:+T=4,
+phiX174	1451	.	G	.	.	.	AC=.;AF=.;SB=0.0	GT:AC:AF:SB:NC	0/0:.:.:0.0:+G=3,
+phiX174	1452	.	A	.	.	.	AC=.;AF=.;SB=0.0	GT:AC:AF:SB:NC	0/0:.:.:0.0:+A=2,
+phiX174	1453	.	G	.	.	.	AC=.;AF=.;SB=0.0	GT:AC:AF:SB:NC	0/0:.:.:0.0:+G=1,