# HG changeset patch
# User iuc
# Date 1750337865 0
# Node ID 85a38dffb93d009f6b06a97a7d752789f5bcd1f4
# Parent  18dbde5680c0b9ff10bf45b8e618ed8f8be81010
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_cram commit c508c3af0f4121dcc38e0be63db00a604e997b8a

diff -r 18dbde5680c0 -r 85a38dffb93d macros.xml
--- a/macros.xml	Sun Sep 08 03:24:49 2024 +0000
+++ b/macros.xml	Thu Jun 19 12:57:45 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 18dbde5680c0 -r 85a38dffb93d samtools_bam_to_cram.xml
--- a/samtools_bam_to_cram.xml	Sun Sep 08 03:24:49 2024 +0000
+++ b/samtools_bam_to_cram.xml	Thu Jun 19 12:57:45 2025 +0000
@@ -59,39 +59,59 @@
     <tests>
         <test>
             <param name="input" value="test.bam" ftype="bam" />
-            <param name="addref_select" value="history" />
-            <param name="ref" value="test.fa" />
-            <param name="target_region" value="entire_input_file" />
+            <conditional name="addref_cond">
+                <param name="addref_select" value="history" />
+                <param name="ref" value="test.fa" />
+            </conditional>
+            <conditional name="parameter_regions">
+                <param name="target_region" value="entire_input_file" />
+            </conditional>
             <output name="output_alignment" file="test_bam.cram" ftype="cram" compare="sim_size" delta="250" />
         </test>
         <test>
             <param name="input" value="test.sam" ftype="sam" />
-            <param name="addref_select" value="history" />
-            <param name="ref" value="test.fa" />
-            <param name="target_region" value="entire_input_file" />
+            <conditional name="addref_cond">
+                <param name="addref_select" value="history" />
+                <param name="ref" value="test.fa" />
+            </conditional>
+            <conditional name="parameter_regions">
+                <param name="target_region" value="entire_input_file" />
+            </conditional>
             <output name="output_alignment" file="test_sam.cram" ftype="cram" compare="sim_size" delta="250" />
         </test>
         <test>
             <param name="input" value="test.bam" ftype="bam" />
-            <param name="addref_select" value="history" />
-            <param name="ref" value="test.fa" />
-            <param name="target_region" value="region" />
-            <param name="region_string" value="CHROMOSOME_I" />
+            <conditional name="addref_cond">
+                <param name="addref_select" value="history" />
+                <param name="ref" value="test.fa" />
+            </conditional>
+            <conditional name="parameter_regions">
+                <param name="target_region" value="region" />
+                <param name="region_string" value="CHROMOSOME_I" />
+            </conditional>
             <output name="output_alignment" file="test_chr1.cram" ftype="cram" compare="sim_size" delta="250" />
         </test>
         <test>
             <param name="input" value="test.bam" ftype="bam" />
-            <param name="addref_select" value="history" />
-            <param name="ref" value="test.fa" />
-            <param name="target_region" value="regions_bed_file" />
-            <param name="regions_bed_file" value="test.bed" ftype="bed" />
+            <conditional name="addref_cond">
+                <param name="addref_select" value="history" />
+                <param name="ref" value="test.fa" />
+            </conditional>
+            <conditional name="parameter_regions">
+                <param name="target_region" value="regions_bed_file" />
+                <param name="regions_bed_file" value="test.bed" ftype="bed" />
+            </conditional>
             <output name="output_alignment" file="test_regions.cram" ftype="cram" compare="sim_size" delta="250" />
         </test>
         <test>
             <param name="input" ftype="bam" dbkey="equCab2" value="sam_to_bam_out2.bam" />
-            <param name="addref_select" value="cached" />
-            <param name="ref" value="equCab2chrM" />
-            <param name="target_region" value="entire_input_file" />
+            <conditional name="addref_cond">
+                <param name="addref_select" value="cached" />
+                <param name="ref" value="equCab2chrM" />
+            </conditional>
+            <conditional name="parameter_regions">
+                <param name="target_region" value="entire_input_file" />
+            </conditional>
             <output name="output_alignment" file="test2.cram" ftype="cram" compare="sim_size" delta="250" />
         </test>
     </tests>