# HG changeset patch
# User iuc
# Date 1657099582 0
# Node ID 791f73caa0c869585a15a92fdedbf33c18b287bc
# Parent  09d6e46938872b2f04087088a2f772fc6ee4b62b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3751719cd03b8380954e2231cf91496c863056e2

diff -r 09d6e4693887 -r 791f73caa0c8 lofreq_alnqual.xml
--- a/lofreq_alnqual.xml	Mon Oct 05 20:14:58 2020 +0000
+++ b/lofreq_alnqual.xml	Wed Jul 06 09:26:22 2022 +0000
@@ -1,4 +1,4 @@
-<tool id="lofreq_alnqual" name="Add LoFreq alignment quality scores" version="@TOOL_VERSION@+galaxy0" profile="18.01">
+<tool id="lofreq_alnqual" name="Add LoFreq alignment quality scores" version="@TOOL_VERSION@+galaxy1" profile="18.01">
     <description>to aligned read SAM/BAM records</description>
     <macros>
         <import>macros.xml</import>
@@ -23,7 +23,7 @@
             <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="output" file="alnqual-out1.bam" />
+            <output name="output" file="alnqual-out1.bam" ftype="bam" />
         </test>
         <test>
             <param name="reads" ftype="bam" value="lofreq-in1.bam" />
@@ -32,7 +32,7 @@
             <conditional name="alnqual_choice">
                 <param name="alnquals_to_use" value="-B" />
             </conditional>
-            <output name="output" file="alnqual-out2.bam" />
+            <output name="output" file="alnqual-out2.bam" ftype="bam" />
         </test>
         <test>
             <param name="reads" ftype="bam" value="lofreq-in1.bam" />
@@ -41,7 +41,7 @@
             <conditional name="alnqual_choice">
                 <param name="alnquals_to_use" value="-A" />
             </conditional>
-            <output name="output" file="alnqual-out3.bam" />
+            <output name="output" file="alnqual-out3.bam" ftype="bam" />
         </test>
         <test>
             <param name="reads" ftype="bam" value="lofreq-in1.bam" />
@@ -50,14 +50,14 @@
             <conditional name="alnqual_choice">
                 <param name="extended_baq" value="false" />
             </conditional>
-            <output name="output" file="alnqual-out4.bam" />
+            <output name="output" file="alnqual-out4.bam" ftype="bam" />
         </test>
         <test>
             <param name="reads" ftype="bam" value="lofreq-in1.bam" />
             <param name="ref_selector" value="history" />
             <param name="ref" ftype="fasta" value="pBR322.fa" />
             <param name="recompute" value="true" />
-            <output name="output" file="alnqual-out5.bam" />
+            <output name="output" file="alnqual-out5.bam" ftype="bam" />
         </test>
     </tests>
     <help><![CDATA[