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changeset 12:d60c3f704da0 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6b8fbd9db12329e2f49eee672b185015c3e35d4f
author iuc
date Tue, 13 Aug 2024 12:18:39 +0000
parents c59d48774d03
children dbfc505896e9
files fastp.xml macros.xml
diffstat 2 files changed, 8 insertions(+), 3 deletions(-) [+]
line wrap: on
line diff
--- a/fastp.xml	Tue Mar 05 08:41:43 2024 +0000
+++ b/fastp.xml	Tue Aug 13 12:18:39 2024 +0000
@@ -1,4 +1,4 @@
-<tool id="fastp" name="fastp" version="@TOOL_VERSION@+galaxy0" profile="23.1">
+<tool id="fastp" name="fastp" version="@TOOL_VERSION@+galaxy1" profile="23.1">
     <description>fast all-in-one preprocessing for FASTQ files</description>
     <macros>
         <import>macros.xml</import>
@@ -73,9 +73,8 @@
 #if str($single_paired.single_paired_selector).startswith('paired'):
     #if str($single_paired.adapter_trimming_options.adapter_sequence2):
         --adapter_sequence_r2 '$single_paired.adapter_trimming_options.adapter_sequence2'
-    #else
-        --detect_adapter_for_pe
     #end if
+    $single_paired.adapter_trimming_options.detect_adapter_for_pe
 #end if
 
 
@@ -226,6 +225,7 @@
                 <expand macro="in" read_number="2" argument="-I"/>
                 <expand macro="adapter_trimming_options">
                     <expand macro="adapter_sequence" read_number="2"/>
+                    <expand macro="detect_adapter_for_pe" />
                 </expand>
                 <expand macro="global_trimming_options_paired" />
             </when>
@@ -233,6 +233,7 @@
                 <param name="paired_input" type="data_collection" format="fastq,fastq.gz" label="Select paired collection(s)" collection_type="paired"/>
                 <expand macro="adapter_trimming_options">
                     <expand macro="adapter_sequence" read_number="2"/>
+                    <expand macro="detect_adapter_for_pe" />
                 </expand>
                 <expand macro="global_trimming_options_paired" />
             </when>
--- a/macros.xml	Tue Mar 05 08:41:43 2024 +0000
+++ b/macros.xml	Tue Aug 13 12:18:39 2024 +0000
@@ -43,6 +43,10 @@
         </param>
     </xml>
 
+    <xml name="detect_adapter_for_pe">
+        <param argument="--detect_adapter_for_pe" type="boolean" truevalue="--detect_adapter_for_pe" falsevalue="" checked="false" label="Adapter sequence auto-detection for paired-end" />
+    </xml>
+
     <xml name="in" token_read_number="1" token_argument="-i">
         <param name="in@READ_NUMBER@" argument="@ARGUMENT@" type="data" format="fastq,fastq.gz" label="Input @READ_NUMBER@" help="Input FASTQ file #@READ_NUMBER@"/>
     </xml>