Mercurial > repos > devteam > fastq_paired_end_deinterlacer

changeset 6:c48cf4699be7 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer commit a5766d27dcddd1891766476a913d0eae1ec7a3c9
author iuc
date Sun, 23 Nov 2025 17:50:37 +0000
parents 523c2aff0376
children
files fastq_paired_end_deinterlacer.xml macros.xml
diffstat 2 files changed, 24 insertions(+), 17 deletions(-) [+]
line wrap: on
line diff
--- a/fastq_paired_end_deinterlacer.xml	Fri Oct 04 10:34:55 2024 +0000
+++ b/fastq_paired_end_deinterlacer.xml	Sun Nov 23 17:50:37 2025 +0000
@@ -11,43 +11,50 @@
     </edam_operations>
     <expand macro="requirements"/>
     <command><![CDATA[
-gx-fastq-paired-end-deinterlacer '$input_file' '${input_file.extension[len('fastq'):]}' '$output1_pairs_file' '$output2_pairs_file' '$output1_singles_file' '$output2_singles_file'
+gx-fastq-paired-end-deinterlacer '$input_file' '${input_file.extension[len('fastq'):]}' '$pairs.forward' '$pairs.reverse' '$output1_singles_file' '$output2_singles_file'
     ]]></command>
     <inputs>
         <param name="input_file" type="data" format="fastqsanger,fastqcssanger,fastqsanger.gz,fastqcssanger.gz,fastqsanger.bz2,fastqcssanger.bz2" label="FASTQ reads" />
     </inputs>
     <outputs>
-        <data name="output1_pairs_file" format_source="input_file" label="FASTQ de-interlacer left mates from data ${input_file.hid}" />
-        <data name="output2_pairs_file" format_source="input_file" label="FASTQ de-interlacer right mates from data ${input_file.hid}"/>
-        <data name="output1_singles_file" format_source="input_file" label="FASTQ de-interlacer left singles from data ${input_file.hid}"/>
-        <data name="output2_singles_file" format_source="input_file" label="FASTQ de-interlacer right singles from data ${input_file.hid}"/>
+        <collection name="pairs" format_source="input_file" type="paired" label="${tool.name} on ${on_string}: pairs"/>
+        <data name="output1_singles_file" format_source="input_file" label="${tool.name} on ${on_string}: left singles"/>
+        <data name="output2_singles_file" format_source="input_file" label="${tool.name} on ${on_string}: right singles"/>
     </outputs>
     <tests>
         <test>
             <param name="input_file" value="paired_end_merged.fastqsanger" ftype="fastqsanger" />
-            <output name="output1_pairs_file" file="paired_end_1.fastqsanger" ftype="fastqsanger" />
-            <output name="output2_pairs_file" file="paired_end_2.fastqsanger" ftype="fastqsanger" />
+            <output_collection name="pairs">
+                <element name="forward" value="paired_end_1.fastqsanger" ftype="fastqsanger"/>
+                <element name="reverse" value="paired_end_2.fastqsanger" ftype="fastqsanger"/>
+            </output_collection>
             <output name="output1_singles_file" file="paired_end_1_singles.fastqsanger" ftype="fastqsanger" />
             <output name="output2_singles_file" file="paired_end_2_singles.fastqsanger" ftype="fastqsanger" />
         </test>
         <test>
             <param name="input_file" value="paired_end_merged_errors.fastqsanger" ftype="fastqsanger" />
-            <output name="output1_pairs_file" file="paired_end_1_cleaned.fastqsanger" ftype="fastqsanger" />
-            <output name="output2_pairs_file" file="paired_end_2_cleaned.fastqsanger" ftype="fastqsanger" />
+            <output_collection name="pairs">
+                <element name="forward" value="paired_end_1_cleaned.fastqsanger" ftype="fastqsanger"/>
+                <element name="reverse" value="paired_end_2_cleaned.fastqsanger" ftype="fastqsanger"/>
+            </output_collection>
             <output name="output1_singles_file" file="paired_end_1_cleaned_singles.fastqsanger" ftype="fastqsanger" />
             <output name="output2_singles_file" file="paired_end_2_cleaned_singles.fastqsanger" ftype="fastqsanger" />
         </test>
         <test>
             <param name="input_file" value="paired_end_merged_errors.fastqsanger.gz" ftype="fastqsanger.gz" />
-            <output name="output1_pairs_file" file="paired_end_1_cleaned.fastqsanger" ftype="fastqsanger.gz" decompress="true" />
-            <output name="output2_pairs_file" file="paired_end_2_cleaned.fastqsanger" ftype="fastqsanger.gz" decompress="true" />
+            <output_collection name="pairs">
+                <element name="forward" value="paired_end_1_cleaned.fastqsanger" ftype="fastqsanger.gz" decompress="true"/>
+                <element name="reverse" value="paired_end_2_cleaned.fastqsanger" ftype="fastqsanger.gz" decompress="true"/>
+            </output_collection>
             <output name="output1_singles_file" file="paired_end_1_cleaned_singles.fastqsanger" ftype="fastqsanger.gz" decompress="true" />
             <output name="output2_singles_file" file="paired_end_2_cleaned_singles.fastqsanger" ftype="fastqsanger.gz" decompress="true" />
         </test>
         <test>
             <param name="input_file" value="paired_end_merged_errors.fastqsanger.bz2" ftype="fastqsanger.bz2" />
-            <output name="output1_pairs_file" file="paired_end_1_cleaned.fastqsanger" ftype="fastqsanger.bz2" decompress="true" />
-            <output name="output2_pairs_file" file="paired_end_2_cleaned.fastqsanger" ftype="fastqsanger.bz2" decompress="true" />
+            <output_collection name="pairs">
+                <element name="forward" value="paired_end_1_cleaned.fastqsanger" ftype="fastqsanger.bz2" decompress="true"/>
+                <element name="reverse" value="paired_end_2_cleaned.fastqsanger" ftype="fastqsanger.bz2" decompress="true"/>
+            </output_collection>
             <output name="output1_singles_file" file="paired_end_1_cleaned_singles.fastqsanger" ftype="fastqsanger.bz2" decompress="true" />
             <output name="output2_singles_file" file="paired_end_2_cleaned_singles.fastqsanger" ftype="fastqsanger.bz2" decompress="true" />
         </test>
--- a/macros.xml	Fri Oct 04 10:34:55 2024 +0000
+++ b/macros.xml	Sun Nov 23 17:50:37 2025 +0000
@@ -1,11 +1,11 @@
 <macros>
-    <token name="@TOOL_VERSION@">1.1.5</token>
-    <token name="@VERSION_SUFFIX@">2</token>
-    <token name="@PROFILE@">23.1</token>
+    <token name="@TOOL_VERSION@">1.2</token>
+    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@PROFILE@">24.2</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">galaxy_sequence_utils</requirement>
             <yield/>
         </requirements>
-    </xml>>
+    </xml>
 </macros>