# HG changeset patch
# User iuc
# Date 1584802324 14400
# Node ID 3b4b2121842f8aa1d0580fffb4714126023e9ea0
# Parent  dfadc322b065f0092cbd9f90032a80d26abd5a59
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 53bf37f3bf192c4a9d14f2055f106b429cf7b5c1"

diff -r dfadc322b065 -r 3b4b2121842f lofreq_call.xml
--- a/lofreq_call.xml	Wed Feb 12 18:45:42 2020 -0500
+++ b/lofreq_call.xml	Sat Mar 21 10:52:04 2020 -0400
@@ -1,4 +1,4 @@
-<tool id="lofreq_call" name="Call variants" version="@TOOL_VERSION@+galaxy1">
+<tool id="lofreq_call" name="Call variants" version="@TOOL_VERSION@+galaxy2">
     <description>with LoFreq</description>
     <macros>
         <import>macros.xml</import>
@@ -126,10 +126,10 @@
         </conditional>
         <param name="variant_types" type="select"
         label="Types of variants to call"
-        help="Note: When including indels in the called variants you should preprocess your input data to include indel alignment qualities">
+        help="Note: To have indels included in the called variants you HAVE to preprocess your input data using lofreq indelqual to include indel qualities. In addition, it is highly recommended that you calculate and make use of indel alignment qualities. See the detailed tool help below.">
             <option value="--call-indels">SNVs and indels</option>
             <option value="" selected="True">Only SNVs</option>
-            <option value="--only-indels">Only indels</option>
+            <option value="--call-indels --only-indels">Only indels</option>
         </param>
         <conditional name="call_control">
             <param name="set_call_options" type="select"
@@ -326,6 +326,16 @@
             </conditional>
             <output name="variants" file="call-out2.vcf" lines_diff="4" />
         </test>
+        <test>
+            <param name="reads" ftype="bam" value="indelqual-out3.bam" />
+            <param name="ref_selector" value="history" />
+            <param name="ref" ftype="fasta" value="pBR322.fa" />
+            <param name="variant_types" value="--call-indels --only-indels" />
+            <conditional name="filter_control">
+                <param name="filter_type" value="set_all_off" />
+            </conditional>
+            <output name="variants" file="indel-call-out.vcf" lines_diff="4" />
+        </test>
     </tests>
     <help><![CDATA[
 lofreq call: call variants from BAM file
@@ -364,7 +374,7 @@
   responsible for adding indel qualitites, which are required for indel
   calling with lofreq, to your input.
 
-  For doing so, you can use ``lofreq indelqual`` or GATK's BQSR.
+  For doing so, you can use ``lofreq indelqual``.
 
 - Base/indel alignment quality
 
diff -r dfadc322b065 -r 3b4b2121842f test-data/indel-call-out.vcf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/indel-call-out.vcf	Sat Mar 21 10:52:04 2020 -0400
@@ -0,0 +1,21 @@
+##fileformat=VCFv4.0
+##fileDate=20200320
+##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/tmppZpVLj/job_working_directory/000/9/working/pp-tmp/lofreq2_call_parallele60ipsuv/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">
+##INFO=<ID=SB,Number=1,Type=Integer,Description="Phred-scaled strand bias at this position">
+##INFO=<ID=DP4,Number=4,Type=Integer,Description="Counts for ref-forward bases, ref-reverse, alt-forward and alt-reverse bases">
+##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
+##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	.	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