Mercurial > repos > iuc > umi_tools_count

changeset 14:43bcc103b1e9 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit 11a7415c7f8a44a3f990080533c1de43a41d1e2e
author iuc
date Fri, 28 Feb 2025 20:40:52 +0000
parents 437d5c72f2e3
children
files macros.xml test-data/dedup_out1.bam test-data/dedup_out2.bam test-data/dedup_out3.bam test-data/dedup_out4.bam test-data/dedup_out5.bam test-data/dedup_out6.bam umi-tools_counts.xml
diffstat 8 files changed, 6 insertions(+), 7 deletions(-) [+]
line wrap: on
line diff
--- 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">
Binary file test-data/dedup_out1.bam has changed
Binary file test-data/dedup_out2.bam has changed
Binary file test-data/dedup_out3.bam has changed
Binary file test-data/dedup_out4.bam has changed
Binary file test-data/dedup_out5.bam has changed
Binary file test-data/dedup_out6.bam has changed
--- 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@