# HG changeset patch
# User iuc
# Date 1750337924 0
# Node ID ddbd49b892e5358913d4b53f09999c69e4dc39e9
# Parent  f4f7f632815d516eeaad6dd474e7eff8c2f1aaa5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit c508c3af0f4121dcc38e0be63db00a604e997b8a

diff -r f4f7f632815d -r ddbd49b892e5 macros.xml
--- a/macros.xml	Fri May 16 12:57:31 2025 +0000
+++ b/macros.xml	Thu Jun 19 12:58:44 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 f4f7f632815d -r ddbd49b892e5 samtools_coverage.xml
--- a/samtools_coverage.xml	Fri May 16 12:57:31 2025 +0000
+++ b/samtools_coverage.xml	Thu Jun 19 12:58:44 2025 +0000
@@ -100,31 +100,49 @@
 
     <tests>
         <test>
-            <param name="input" value="test_1.bam" ftype="bam" />
+            <conditional name="condition_input">
+                <param name="input" value="test_1.bam" ftype="bam" />
+            </conditional>
             <output name="output" file="results_1.tabular" ftype="tabular" />
         </test>
         <test>
-            <param name="input" value="test_1.bam" ftype="bam" />
-            <param name="histogram_select" value="yes" />
-            <param name="n_bins" value="50" />
+            <conditional name="condition_input">
+                <param name="input" value="test_1.bam" ftype="bam" />
+            </conditional>
+            <conditional name="condition_histogram">
+                <param name="histogram_select" value="yes" />
+                <param name="n_bins" value="50" />
+            </conditional>
             <output name="output" file="results_2.txt" ftype="tabular" />
         </test>
         <test>
-            <param name="input_pooling" value="Yes" />
-            <param name="input_bams" value="test_1.bam,test_2.bam" ftype="bam" />
-            <param name="histogram_select" value="yes" />
-            <param name="n_bins" value="100" />
+            <conditional name="condition_input">
+                <param name="input_pooling" value="Yes" />
+                <param name="input_bams" value="test_1.bam,test_2.bam" ftype="bam" />
+            </conditional>
+            <conditional name="condition_histogram">
+                <param name="histogram_select" value="yes" />
+                <param name="n_bins" value="100" />
+            </conditional>
             <output name="output" file="results_3.txt" ftype="tabular" />
         </test>
         <test><!-- test with a region (requires index) -->
-            <param name="input" value="test_1.bam" ftype="bam" />
-            <param name="region" value="ref1" />
+            <conditional name="condition_input">
+                <param name="input" value="test_1.bam" ftype="bam" />
+            </conditional>
+            <section name="additional_options">
+                <param name="region" value="ref1" />
+            </section>
             <output name="output" file="results_4.tabular" ftype="tabular" />
         </test>
         <test><!-- test with pooled BAMs and a region -->
-            <param name="input_pooling" value="Yes" />
-            <param name="input_bams" value="test_1.bam,test_2.bam" ftype="bam" />
-            <param name="region" value="ref2" />
+            <conditional name="condition_input">
+                <param name="input_pooling" value="Yes" />
+                <param name="input_bams" value="test_1.bam,test_2.bam" ftype="bam" />
+            </conditional>
+            <section name="additional_options">
+                <param name="region" value="ref2" />
+            </section>
             <output name="output" file="results_5.tabular" ftype="tabular" />
         </test>
     </tests>