diff umi-tools_extract.xml @ 19:7a7e33d28f62 draft default tip

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

--- a/umi-tools_extract.xml	Sat Sep 28 16:39:41 2024 +0000
+++ b/umi-tools_extract.xml	Sat Oct 05 13:07:19 2024 +0000
@@ -1,9 +1,9 @@
 <tool id="umi_tools_extract" name="UMI-tools extract" 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" />
     <command detect_errors="exit_code"><![CDATA[
     @COMMAND_LINK@
@@ -111,10 +111,10 @@
         <expand macro="log_input_macro"/>
     </inputs>
     <outputs>
-        <data name="out" format_source="input_read1" label="${tool.name} on ${on_string}: Reads" >
+        <data name="out" format_source="input_read1" label="${tool.name} on ${on_string}: Forward reads" >
             <filter>input_type_cond['input_type'] in ['single', 'paired']</filter>
         </data>
-        <data name="out2" format_source="input_read2" label="${tool.name} on ${on_string}: Reads2" >
+        <data name="out2" format_source="input_read2" label="${tool.name} on ${on_string}: Reverse reads" >
             <filter>input_type_cond['input_type'] == 'paired'</filter>
         </data>
         <collection name="out_paired_collection" type="paired" label="${tool.name} on ${on_string}: Reads">
@@ -136,7 +136,6 @@
             </conditional>
             <param name="quality_selector" value="true" />
             <param name="quality_filter_threshold" value="10" />
-            <param name="quality_encoding" value="phred33" />
             <param name="log" value="true"/>
             <output name="out" file="out_SE.fastq" ftype="fastqsanger" />
             <output name="out_log" >