Mercurial > repos > devteam > sam_to_bam

diff sam_to_bam.xml @ 14:73913bb77da3 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit c508c3af0f4121dcc38e0be63db00a604e997b8a
author iuc
date Thu, 19 Jun 2025 12:58:11 +0000
parents 9bd1568619cd
children 72b8a3614802
line wrap: on
line diff
--- a/sam_to_bam.xml	Sun Sep 08 03:25:11 2024 +0000
+++ b/sam_to_bam.xml	Thu Jun 19 12:58:11 2025 +0000
@@ -1,4 +1,4 @@
-<tool id="sam_to_bam" name="SAM-to-BAM" version="2.1.2" profile="@PROFILE@">
+<tool id="sam_to_bam" name="SAM-to-BAM" version="2.1.3" profile="@PROFILE@">
     <description>convert SAM to BAM</description>
 
     <macros>
@@ -50,34 +50,44 @@
     </outputs>
     <tests>
         <test>
-            <param name="addref_select" value="history" />
-            <param name="ref" ftype="fasta" dbkey="equCab2" value="chr_m.fasta" />
+            <conditional name="addref_cond">
+                <param name="addref_select" value="history" />
+                <param name="ref" ftype="fasta" dbkey="equCab2" value="chr_m.fasta" />
+            </conditional>
             <param name="input" ftype="sam" value="sam_to_bam_in1.sam" />
             <output name="output1" ftype="bam" file="sam_to_bam_out1.bam" lines_diff="4"/>
         </test>
         <test>
-            <param name="addref_select" value="cached" />
-            <param name="ref" value="equCab2chrM" />
+            <conditional name="addref_cond">
+                <param name="addref_select" value="cached" />
+                <param name="ref" value="equCab2chrM" />
+            </conditional>
             <param name="input" ftype="sam" dbkey="equCab2" value="sam_to_bam_in1.sam" />
             <output name="output1" ftype="bam" file="sam_to_bam_out2.bam" lines_diff="4"/>
         </test>
         <test>
-            <param name="addref_select" value="history" />
-            <param name="ref" ftype="fasta" dbkey="equCab2" value="chr_m.fasta" />
+            <conditional name="addref_cond">
+                <param name="addref_select" value="history" />
+                <param name="ref" ftype="fasta" dbkey="equCab2" value="chr_m.fasta" />
+            </conditional>
             <param name="input" ftype="sam" value="sam_to_bam_noheader_in2.sam" />
             <output name="output1" ftype="bam" file="sam_to_bam_out3.bam" lines_diff="4"/>
         </test>
         <test>
             <!-- Test direct use of bgzipped reference -->
-            <param name="addref_select" value="history" />
-            <param name="ref" ftype="fasta.gz" dbkey="equCab2" value="chr_m.bgzipped_fasta.gz" />
+            <conditional name="addref_cond">
+                <param name="addref_select" value="history" />
+                <param name="ref" ftype="fasta.gz" dbkey="equCab2" value="chr_m.bgzipped_fasta.gz" />
+            </conditional>
             <param name="input" ftype="sam" value="sam_to_bam_noheader_in2.sam" />
             <output name="output1" ftype="bam" file="sam_to_bam_out3.bam" lines_diff="4"/>
         </test>
         <test>
             <!-- Test with simple gzipped reference, which requires decompression -->
-            <param name="addref_select" value="history" />
-            <param name="ref" ftype="fasta.gz" dbkey="equCab2" value="chr_m.fasta.gz" />
+            <conditional name="addref_cond">
+                <param name="addref_select" value="history" />
+                <param name="ref" ftype="fasta.gz" dbkey="equCab2" value="chr_m.fasta.gz" />
+            </conditional>
             <param name="input" ftype="sam" value="sam_to_bam_noheader_in2.sam" />
             <output name="output1" ftype="bam" file="sam_to_bam_out3.bam" lines_diff="4"/>
         </test>