# HG changeset patch
# User iuc
# Date 1750338064 0
# Node ID fea1a167b822c8eb0ce04636a160eb1f06d936a1
# Parent  b8beef827165fdd5f79e79956a10fe224a3f5021
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_slice_bam commit c508c3af0f4121dcc38e0be63db00a604e997b8a

diff -r b8beef827165 -r fea1a167b822 macros.xml
--- a/macros.xml	Sun Sep 08 03:26:35 2024 +0000
+++ b/macros.xml	Thu Jun 19 13:01:04 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 b8beef827165 -r fea1a167b822 samtools_slice_bam.xml
--- a/samtools_slice_bam.xml	Sun Sep 08 03:26:35 2024 +0000
+++ b/samtools_slice_bam.xml	Thu Jun 19 13:01:04 2025 +0000
@@ -1,4 +1,4 @@
-<tool id="samtools_slice_bam" name="Slice" version="2.0.3" profile="@PROFILE@">
+<tool id="samtools_slice_bam" name="Slice" version="2.0.4" profile="@PROFILE@">
     <description>BAM by genomic regions</description>
     <macros>
         <import>macros.xml</import>
@@ -81,22 +81,30 @@
     <tests>
         <test>
             <param name="input_bam" ftype="bam" value="bam-slice-input.bam" />
-            <param name="slice_method_selector" value="bed"/>
-            <param name="input_interval" ftype="bed" value="bam-slice.bed" />
+            <conditional name="slice_method">
+                <param name="slice_method_selector" value="bed"/>
+                <param name="input_interval" ftype="bed" value="bam-slice.bed" />
+            </conditional>
             <output name="output_bam" file="bam-slice-test1.bam" ftype="bam" lines_diff="4" />
         </test>
         <test>
             <param name="input_bam" ftype="bam" value="bam-slice-input.bam" />
-            <param name="slice_method_selector" value="chr"/>
-            <param name="refs" value="chrM" />
+            <conditional name="slice_method">
+                <param name="slice_method_selector" value="chr"/>
+                <param name="refs" value="chrM" />
+            </conditional>
             <output name="output_bam" file="bam-slice-test2.bam" ftype="bam" lines_diff="4" />
         </test>
         <test>
             <param name="input_bam" ftype="bam" value="bam-slice-input.bam" />
-            <param name="slice_method_selector" value="man"/>
-            <param name="chrom" value="chrM" />
-            <param name="start" value="1" />
-            <param name="end" value="1000" />
+            <conditional name="slice_method">
+                <param name="slice_method_selector" value="man"/>
+                <repeat name="regions">
+                    <param name="chrom" value="chrM" />
+                    <param name="start" value="1" />
+                    <param name="end" value="1000" />
+                </repeat>
+            </conditional>
             <output name="output_bam" file="bam-slice-test3.bam" ftype="bam" lines_diff="4"/>
         </test>
     </tests>