# HG changeset patch
# User iuc
# Date 1592241230 14400
# Node ID af7e416d8176b7f26e0af5aba8614aef17148108
# Parent  dbd9f2db9ed883c838c57271b3c300a02716eca3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 841c48994eb214a2f8718b1d1aca22bc38598528"

diff -r dbd9f2db9ed8 -r af7e416d8176 lofreq_viterbi.xml
--- a/lofreq_viterbi.xml	Fri May 29 15:24:28 2020 -0400
+++ b/lofreq_viterbi.xml	Mon Jun 15 13:13:50 2020 -0400
@@ -1,28 +1,26 @@
-<tool id="lofreq_viterbi" name="Realign reads" version="@TOOL_VERSION@+galaxy1">
+<tool id="lofreq_viterbi" name="Realign reads" version="@TOOL_VERSION@+galaxy0">
     <description>with LoFreq viterbi</description>
     <macros>
         <import>macros.xml</import>
     </macros>
-    <expand macro="requirements">
-        <requirement type="package" version="1.9">samtools</requirement>
-    </expand>
+    <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
         @PREPARE_REF@
         lofreq viterbi
         --ref '$reference_fasta_fn'
-        ${adv_options.delflags}
+        ${adv_options.keepflags}
         --defqual ${adv_options.bq2_handling.defqual}
         --out tmp.bam '$reads' &&
 
-        samtools sort -T "\${TMPDIR:-.}" -@ \${GALAXY_SLOTS:-1} -O BAM -o '$realigned' tmp.bam
+        samtools sort --no-PG -T "\${TMPDIR:-.}" -@ \${GALAXY_SLOTS:-1} -O BAM -o '$realigned' tmp.bam
     ]]></command>
     <inputs>
         <param name="reads" type="data" format="bam" label="Reads to realign" />
         <expand macro="reference_interface" />
         <section name="adv_options" title="Advanced options" expanded="false">
-            <param argument="--keepflags" name="delflags" type="boolean" truevalue="" falsevalue="--keepflags" checked="true"
-            label="Delete flags MC, MD, NM, and A?"
-            help="These flags are all prone to getting invalidated during realignment. Keep them only if you know what you are doing." />
+            <param argument="--keepflags" type="boolean" truevalue="--keepflags" falsevalue="" checked="false"
+            label="Keep MC, MD, NM, and A flags?"
+            help="Re-alignment resets the MC, MD, NM, and A flags by default. The values of these tags depend on the exact alignment. Use this option only if you know what you are doing." />
             <conditional name="bq2_handling">
                 <param name="replace_bq2" type="select"
                 label="How to handle base qualities of 2?"
@@ -51,17 +49,18 @@
         <test>
             <param name="reads" ftype="bam" value="lofreq-in1.bam" />
             <param name="ref_selector" value="history" />
+            <param name="ref_selector" value="history" />
             <param name="ref" ftype="fasta" value="pBR322.fa" />
-            <output name="realigned" file="viterbi-out1.bam" />
+            <output name="realigned" file="viterbi-out1.bam" ftype="bam" />
         </test>
         <test>
             <param name="reads" ftype="bam" value="lofreq-in1.bam" />
             <param name="ref_selector" value="history" />
             <section name="adv_options">
-                <param name="delflags" value="false" />
+                <param name="keepflags" value="true" />
             </section>
             <param name="ref" ftype="fasta" value="pBR322.fa" />
-            <output name="realigned" file="viterbi-out2.bam" />
+            <output name="realigned" file="viterbi-out2.bam" ftype="bam" />
         </test>
     </tests>
     <help><![CDATA[
diff -r dbd9f2db9ed8 -r af7e416d8176 macros.xml
--- a/macros.xml	Fri May 29 15:24:28 2020 -0400
+++ b/macros.xml	Mon Jun 15 13:13:50 2020 -0400
@@ -1,11 +1,11 @@
 <macros>
-    <token name="@WRAPPER_VERSION@">@TOOL_VERSION@+galaxy</token>
-    <token name="@TOOL_VERSION@">2.1.4</token>
+    <token name="@TOOL_VERSION@">2.1.5</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">lofreq</requirement>
             <yield/>
         </requirements>
+        <version_command>lofreq version | grep version | cut -d ' ' -f 2</version_command>
     </xml>
     <xml name="citations">
         <citations>
diff -r dbd9f2db9ed8 -r af7e416d8176 test-data/call-out1.vcf
--- a/test-data/call-out1.vcf	Fri May 29 15:24:28 2020 -0400
+++ b/test-data/call-out1.vcf	Mon Jun 15 13:13:50 2020 -0400
@@ -1,6 +1,6 @@
 ##fileformat=VCFv4.0
-##fileDate=20200529
-##source=lofreq call --verbose --ref reference.fa --min-cov 1 --max-depth 1000000 --min-bq 6 --min-alt-bq 6 --min-mq 0 --max-mq 255 --src-qual --ign-vcf ign0.vcf --def-nm-q 40 --min-jq 0 --min-alt-jq 0 --def-alt-jq 0 --sig 0.01 --bonf dynamic --no-default-filter -r pBR322:1-2180 -o /tmp/lofreq2_call_parallelqgn6kxdr/0.vcf.gz reads.bam 
+##fileDate=20200615
+##source=lofreq call --verbose --ref reference.fa --sig 1 --bonf 1 --no-default-filter --no-default-filter -r pBR322:1-2180 -o /tmp/tmpe0171355/job_working_directory/000/28/working/pp-tmp/lofreq2_call_parallell2yprl2k/0.vcf.gz reads.bam 
 ##reference=reference.fa
 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw Depth">
 ##INFO=<ID=AF,Number=1,Type=Float,Description="Allele Frequency">
diff -r dbd9f2db9ed8 -r af7e416d8176 test-data/call-out2.vcf
--- a/test-data/call-out2.vcf	Fri May 29 15:24:28 2020 -0400
+++ b/test-data/call-out2.vcf	Mon Jun 15 13:13:50 2020 -0400
@@ -1,6 +1,6 @@
 ##fileformat=VCFv4.0
-##fileDate=20200529
-##source=lofreq call --verbose --ref reference.fa --sig 1 --bonf 1 --no-default-filter --no-default-filter -r pBR322:1-2180 -o /tmp/lofreq2_call_parallelkzkzyltj/0.vcf.gz reads.bam 
+##fileDate=20200615
+##source=lofreq call --verbose --ref reference.fa --sig 1 --bonf 1 --no-default-filter --no-default-filter -r pBR322:1-2180 -o /tmp/tmp265htsdc/job_working_directory/000/28/working/pp-tmp/lofreq2_call_parallelg3dmyvln/0.vcf.gz reads.bam 
 ##reference=reference.fa
 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw Depth">
 ##INFO=<ID=AF,Number=1,Type=Float,Description="Allele Frequency">
diff -r dbd9f2db9ed8 -r af7e416d8176 test-data/indel-call-out.vcf
--- a/test-data/indel-call-out.vcf	Fri May 29 15:24:28 2020 -0400
+++ b/test-data/indel-call-out.vcf	Mon Jun 15 13:13:50 2020 -0400
@@ -1,6 +1,6 @@
 ##fileformat=VCFv4.0
-##fileDate=20200529
-##source=lofreq call --verbose --ref reference.fa --call-indels --only-indels --sig 1 --bonf 1 --no-default-filter --no-default-filter -r pBR322:1-2180 -o /tmp/lofreq2_call_parallelafbznae0/0.vcf.gz reads.bam 
+##fileDate=20200615
+##source=lofreq call --verbose --ref reference.fa --call-indels --only-indels --sig 1 --bonf 1 --no-default-filter --no-default-filter -r pBR322:1-2180 -o /tmp/tmp265htsdc/job_working_directory/000/31/working/pp-tmp/lofreq2_call_parallel4gfado3q/0.vcf.gz reads.bam 
 ##reference=reference.fa
 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw Depth">
 ##INFO=<ID=AF,Number=1,Type=Float,Description="Allele Frequency">
@@ -10,12 +10,12 @@
 ##INFO=<ID=CONSVAR,Number=0,Type=Flag,Description="Indicates that the variant is a consensus variant (as opposed to a low frequency variant).">
 ##INFO=<ID=HRUN,Number=1,Type=Integer,Description="Homopolymer length to the right of report indel position">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
-pBR322	725	.	G	GN	0	.	;HRUN=1
-pBR322	746	.	A	AN	0	.	;HRUN=1
-pBR322	747	.	T	TN	0	.	;HRUN=1
-pBR322	751	.	G	GN	0	.	;HRUN=1
-pBR322	807	.	T	TN	0	.	;HRUN=3
-pBR322	943	.	C	CCG	0	.	;HRUN=1
-pBR322	1152	.	C	CN	0	.	;HRUN=2
-pBR322	1271	.	A	AN	0	.	;HRUN=2
-pBR322	1376	.	A	ANN	0	.	;HRUN=1
+pBR322	725	.	G	GN	0	.	DP=46;AF=0.021739;SB=0;DP4=22,23,0,1;INDEL;HRUN=1
+pBR322	746	.	A	AN	0	.	DP=225;AF=0.004444;SB=3;DP4=116,108,0,1;INDEL;HRUN=1
+pBR322	747	.	T	TN	0	.	DP=230;AF=0.004348;SB=3;DP4=118,111,0,1;INDEL;HRUN=1
+pBR322	751	.	G	GN	0	.	DP=255;AF=0.003922;SB=3;DP4=128,126,0,1;INDEL;HRUN=1
+pBR322	807	.	T	TN	0	.	DP=606;AF=0.001650;SB=0;DP4=300,305,0,1;INDEL;HRUN=3
+pBR322	943	.	C	CCG	0	.	DP=1465;AF=0.000683;SB=0;DP4=709,755,0,1;INDEL;HRUN=1
+pBR322	1152	.	C	CN	0	.	DP=1754;AF=0.000570;SB=0;DP4=926,830,1,0;INDEL;HRUN=2
+pBR322	1271	.	A	AN	0	.	DP=1743;AF=0.000574;SB=0;DP4=890,855,1,0;INDEL;HRUN=2
+pBR322	1376	.	A	ANN	0	.	DP=1691;AF=0.000591;SB=3;DP4=849,843,0,1;INDEL;HRUN=1