# HG changeset patch
# User iuc
# Date 1740775252 0
# Node ID 43bcc103b1e955463584278dc5c65d083e3a33d6
# Parent  437d5c72f2e3bdec9291b5ce6229e1a35eab352d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit 11a7415c7f8a44a3f990080533c1de43a41d1e2e

diff -r 437d5c72f2e3 -r 43bcc103b1e9 macros.xml
--- a/macros.xml	Wed Jan 29 10:08:43 2025 +0000
+++ b/macros.xml	Fri Feb 28 20:40:52 2025 +0000
@@ -9,7 +9,8 @@
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">umi_tools</requirement>
-            <yield />
+            <requirement type="package" version="1.21">samtools</requirement>
+            <requirement type="package" version="4.7">sed</requirement>
         </requirements>
     </xml>
     <xml name="citations">
@@ -551,7 +552,9 @@
     <token name="@GROUPDEDUP_OPTIONS@"><![CDATA[
         $gd.buffer_whole_contig
         $gd.whole_contig
-        $gd.multimapping_detection_method
+        #if $gd.multimapping_detection_method
+            --multimapping-detection-method $gd.multimapping_detection_method
+        #end if
     ]]></token>
     
     <xml name="log_input_macro">
diff -r 437d5c72f2e3 -r 43bcc103b1e9 test-data/dedup_out1.bam
Binary file test-data/dedup_out1.bam has changed
diff -r 437d5c72f2e3 -r 43bcc103b1e9 test-data/dedup_out2.bam
Binary file test-data/dedup_out2.bam has changed
diff -r 437d5c72f2e3 -r 43bcc103b1e9 test-data/dedup_out3.bam
Binary file test-data/dedup_out3.bam has changed
diff -r 437d5c72f2e3 -r 43bcc103b1e9 test-data/dedup_out4.bam
Binary file test-data/dedup_out4.bam has changed
diff -r 437d5c72f2e3 -r 43bcc103b1e9 test-data/dedup_out5.bam
Binary file test-data/dedup_out5.bam has changed
diff -r 437d5c72f2e3 -r 43bcc103b1e9 test-data/dedup_out6.bam
Binary file test-data/dedup_out6.bam has changed
diff -r 437d5c72f2e3 -r 43bcc103b1e9 umi-tools_counts.xml
--- a/umi-tools_counts.xml	Wed Jan 29 10:08:43 2025 +0000
+++ b/umi-tools_counts.xml	Fri Feb 28 20:40:52 2025 +0000
@@ -4,11 +4,7 @@
         <import>macros.xml</import>
     </macros>
     <expand macro="bio_tools"/>
-    <expand macro="requirements">
-        <!-- TODO see comment in LINK_SAM_BAM_INPUT -->
-        <requirement type="package" version="1.12">samtools</requirement>
-        <requirement type="package" version="4.7">sed</requirement>
-    </expand>
+    <expand macro="requirements"/>
     <command detect_errors="exit_code"><![CDATA[
         #import re
         @LINK_SAM_BAM_INPUT@