diff umi-tools_dedup.xml @ 16:c5a2ee07c4e1 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bc1b362f6783d3fc0ed0f42c14687001d7ff5f7a

--- a/umi-tools_dedup.xml	Sat Sep 28 16:40:30 2024 +0000
+++ b/umi-tools_dedup.xml	Sat Oct 05 13:08:04 2024 +0000
@@ -1,9 +1,9 @@
 <tool id="umi_tools_dedup" name="UMI-tools deduplicate" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>Extract UMI from fastq files</description>
-    <expand macro="bio_tools"/>
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="bio_tools"/>
     <expand macro="requirements">
         <requirement type="package" version="1.21">samtools</requirement>
     </expand>
@@ -22,7 +22,7 @@
             @FULLSC_OPTIONS@
             @ADVANCED_OPTIONS@
             -I '$input_file' -S deduped.bam
-            ## TODO using samtools sort is a workaround, for the following error that appears when Galaxy
+            ## using samtools sort is a workaround, for the following error that appears when Galaxy
             ## compares the generated file with the one in test-data
             ## `Converting history BAM to SAM failed: 'samtools returned with error 1: stdout=None, stderr=[main_samview] fail to read the header from "/tmp/tmpd8o61jykdedup_out6.bam".\n'. Will compare BAM files`
             ## problem seems to be the BAM file generated with pysam