# HG changeset patch
# User iuc
# Date 1750337891 0
# Node ID 73913bb77da3199d89f9cadca3be3ea663bf1b97
# Parent  0e60e2dd20afdde08b8f26e09897b911d82ba66b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit c508c3af0f4121dcc38e0be63db00a604e997b8a

diff -r 0e60e2dd20af -r 73913bb77da3 macros.xml
--- a/macros.xml	Sun Sep 08 03:25:11 2024 +0000
+++ b/macros.xml	Thu Jun 19 12:58:11 2025 +0000
@@ -11,8 +11,8 @@
          please only bump the minor version in order to let the requirement
          version catch up eventually). To find the tools check:
         `grep "<tool" . -r | grep -v VERSION_SUFFIX | cut -d":" -f 1` -->
-    <token name="@TOOL_VERSION@">1.20</token>
-    <token name="@VERSION_SUFFIX@">2</token>
+    <token name="@TOOL_VERSION@">1.21</token>
+    <token name="@VERSION_SUFFIX@">0</token>
     <token name="@PROFILE@">22.05</token>
     <token name="@FLAGS@"><![CDATA[
         #set $flags = 0
@@ -220,6 +220,7 @@
     <xml name="citations">
         <citations>
             <citation type="doi">10.1093/gigascience/giab008</citation>
+            <citation type="doi">10.1093/bioinformatics/btr076</citation>
         </citations>
     </xml>
     <xml name="version_command">
diff -r 0e60e2dd20af -r 73913bb77da3 sam_to_bam.xml
--- 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>