# HG changeset patch
# User iuc
# Date 1657099557 0
# Node ID 4805fe3d8fdac5605c859dd202c6fe667c72c66f
# Parent  e1461b5c52a01a9681e161a4b6f0af4e598f715d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3751719cd03b8380954e2231cf91496c863056e2

diff -r e1461b5c52a0 -r 4805fe3d8fda lofreq_call.xml
--- a/lofreq_call.xml	Mon Oct 05 20:14:06 2020 +0000
+++ b/lofreq_call.xml	Wed Jul 06 09:25:57 2022 +0000
@@ -1,4 +1,4 @@
-<tool id="lofreq_call" name="Call variants" version="@TOOL_VERSION@+galaxy1" profile="18.01">
+<tool id="lofreq_call" name="Call variants" version="@TOOL_VERSION@+galaxy2" profile="18.01">
     <description>with LoFreq</description>
     <macros>
         <import>macros.xml</import>
@@ -103,6 +103,7 @@
                 && gzip -df variants.vcf.gz
             #end if
         #end if
+        && echo $filter_control.filter_type
     ]]></command>
     <inputs>
         <param type="data" name="reads" format="bam" label="Input reads in BAM format" />
@@ -285,7 +286,13 @@
             <param name="reads" ftype="bam" value="lofreq-in1.bam" />
             <param name="ref_selector" value="history" />
             <param name="ref" ftype="fasta" value="pBR322.fa" />
-            <output name="variants" file="call-out1.vcf" lines_diff="4" />
+            <!-- lines_diff="4" should be sufficient, but https://github.com/CSB5/lofreq/issues/131 -->
+            <output name="variants" file="call-out1.vcf" lines_diff="6" />
+            <assert_command>
+                <has_text text="--sig 0.01"/>
+                <has_text text="--bonf dynamic"/>
+                <has_text text="--no-default-filter" negate="true"/>
+            </assert_command>
         </test>
         <test>
             <param name="reads" ftype="bam" value="lofreq-in1.bam" />
@@ -294,7 +301,8 @@
             <conditional name="call_control">
                 <param name="set_call_options" value="yes" />
             </conditional>
-            <output name="variants" file="call-out1.vcf" lines_diff="4" />
+            <!-- lines_diff="4" should be sufficient, but https://github.com/CSB5/lofreq/issues/131 -->
+            <output name="variants" file="call-out1.vcf" lines_diff="6" />
         </test>
         <test>
             <param name="reads" ftype="bam" value="lofreq-in1.bam" />
@@ -310,7 +318,8 @@
                     </conditional>
                 </section>
             </conditional>
-            <output name="variants" file="call-out1.vcf" lines_diff="4" />
+            <!-- lines_diff="4" should be sufficient, but https://github.com/CSB5/lofreq/issues/131 -->
+            <output name="variants" file="call-out1.vcf" lines_diff="6" />
         </test>
         <test>
             <param name="reads" ftype="bam" value="lofreq-in1.bam" />