Mercurial > repos > devteam > fastq_paired_end_interlacer

changeset 6:e43f96aa1f0e 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_interlacer commit a5766d27dcddd1891766476a913d0eae1ec7a3c9
author iuc
date Sun, 23 Nov 2025 17:49:15 +0000
parents 15fab8bda4e3
children
files fastq_paired_end_interlacer.xml macros.xml
diffstat 2 files changed, 37 insertions(+), 27 deletions(-) [+]
line wrap: on
line diff
--- a/fastq_paired_end_interlacer.xml	Fri Oct 04 10:33:39 2024 +0000
+++ b/fastq_paired_end_interlacer.xml	Sun Nov 23 17:49:15 2025 +0000
@@ -39,56 +39,66 @@
         <!-- $input1_file.name = filename  , e.g. paired_end_2_errors.fastqsanger -->
         <!-- $input1_file.id   = ID        , e.g. 10 -->
         <!-- $input1_file.hid  = history ID, e.g. 5  -->
-        <data name="outfile_pairs" format_source="input1_file" label="FASTQ interlacer pairs from ${on_string}">
+        <data name="outfile_pairs" format_source="input1_file" label="${tool.name} on ${on_string}: pairs">
             <filter>reads['reads_selector'] == 'paired'</filter>
         </data>
-        <data name="outfile_singles" format_source="input1_file" label="FASTQ interlacer singles from ${on_string}">
+        <data name="outfile_singles" format_source="input1_file" label="${tool.name} on ${on_string}: singles">
             <filter>reads['reads_selector'] == 'paired'</filter>
         </data>
-        <data name="outfile_pairs_from_coll" format_source="reads_coll['forward']" label="FASTQ interlacer pairs from ${on_string}">
+        <data name="outfile_pairs_from_coll" format_source="reads_coll['forward']" label="${tool.name} on ${on_string}: pairs">
             <filter>reads['reads_selector'] == 'paired_collection'</filter>
         </data>
-        <data name="outfile_singles_from_coll" format_source="reads_coll['forward']" label="FASTQ interlacer singles from ${on_string}">
+        <data name="outfile_singles_from_coll" format_source="reads_coll['forward']" label="${tool.name} on ${on_string}: singles">
             <filter>reads['reads_selector'] == 'paired_collection'</filter>
         </data>
     </outputs>
     <tests>
         <test expect_num_outputs="2">
-            <param name="reads_selector" value="paired" />
-            <param name="input1_file" value="paired_end_1.fastqsanger" ftype="fastqsanger" />
-            <param name="input2_file" value="paired_end_2.fastqsanger" ftype="fastqsanger" />
+            <conditional name="reads">
+                <param name="reads_selector" value="paired" />
+                <param name="input1_file" value="paired_end_1.fastqsanger" ftype="fastqsanger" />
+                <param name="input2_file" value="paired_end_2.fastqsanger" ftype="fastqsanger" />
+            </conditional>
             <output name="outfile_pairs" file="paired_end_merged.fastqsanger" ftype="fastqsanger" />
             <output name="outfile_singles" file="paired_end_merged_singles.fastqsanger" ftype="fastqsanger" />
         </test>
         <test expect_num_outputs="2">
-            <param name="reads_selector" value="paired" />
-            <param name="input1_file" value="paired_end_1_errors.fastqsanger" ftype="fastqsanger" />
-            <param name="input2_file" value="paired_end_2_errors.fastqsanger" ftype="fastqsanger" />
+            <conditional name="reads">
+                <param name="reads_selector" value="paired" />
+                <param name="input1_file" value="paired_end_1_errors.fastqsanger" ftype="fastqsanger" />
+                <param name="input2_file" value="paired_end_2_errors.fastqsanger" ftype="fastqsanger" />
+            </conditional>
             <output name="outfile_pairs" file="paired_end_merged_cleaned.fastqsanger" ftype="fastqsanger" />
             <output name="outfile_singles" file="paired_end_merged_cleaned_singles.fastqsanger" ftype="fastqsanger" />
         </test>
         <test expect_num_outputs="2">
-            <param name="reads_selector" value="paired" />
-            <param name="input1_file" value="paired_end_1_errors.fastqsanger.gz" ftype="fastqsanger.gz" />
-            <param name="input2_file" value="paired_end_2_errors.fastqsanger.gz" ftype="fastqsanger.gz" />
+            <conditional name="reads">
+                <param name="reads_selector" value="paired" />
+                <param name="input1_file" value="paired_end_1_errors.fastqsanger.gz" ftype="fastqsanger.gz" />
+                <param name="input2_file" value="paired_end_2_errors.fastqsanger.gz" ftype="fastqsanger.gz" />
+            </conditional>
             <output name="outfile_pairs" file="paired_end_merged_cleaned.fastqsanger" ftype="fastqsanger.gz" decompress="true" />
             <output name="outfile_singles" file="paired_end_merged_cleaned_singles.fastqsanger" ftype="fastqsanger.gz" decompress="true" />
         </test>
         <test expect_num_outputs="2">
-            <param name="reads_selector" value="paired" />
-            <param name="input1_file" value="paired_end_1_errors.fastqsanger.bz2" ftype="fastqsanger.bz2" />
-            <param name="input2_file" value="paired_end_2_errors.fastqsanger.bz2" ftype="fastqsanger.bz2" />
+            <conditional name="reads">
+                <param name="reads_selector" value="paired" />
+                <param name="input1_file" value="paired_end_1_errors.fastqsanger.bz2" ftype="fastqsanger.bz2" />
+                <param name="input2_file" value="paired_end_2_errors.fastqsanger.bz2" ftype="fastqsanger.bz2" />
+            </conditional>
             <output name="outfile_pairs" file="paired_end_merged_cleaned.fastqsanger" ftype="fastqsanger.bz2" decompress="true" />
             <output name="outfile_singles" file="paired_end_merged_cleaned_singles.fastqsanger" ftype="fastqsanger.bz2" decompress="true" />
         </test>
         <test expect_num_outputs="2">
-            <param name="reads_selector" value="paired_collection" />
-            <param name="reads_coll">
-                <collection type="paired">
-                    <element name="forward" value="paired_end_1.fastqsanger" ftype="fastqsanger" />
-                    <element name="reverse" value="paired_end_2.fastqsanger" ftype="fastqsanger" />
-                </collection>
-            </param>
+            <conditional name="reads">
+                <param name="reads_selector" value="paired_collection" />
+                <param name="reads_coll">
+                    <collection type="paired">
+                        <element name="forward" value="paired_end_1.fastqsanger" ftype="fastqsanger" />
+                        <element name="reverse" value="paired_end_2.fastqsanger" ftype="fastqsanger" />
+                    </collection>
+                </param>
+            </conditional>
             <output name="outfile_pairs_from_coll" file="paired_end_merged.fastqsanger" ftype="fastqsanger" />
             <output name="outfile_singles_from_coll" file="paired_end_merged_singles.fastqsanger" ftype="fastqsanger" />
         </test>
--- a/macros.xml	Fri Oct 04 10:33:39 2024 +0000
+++ b/macros.xml	Sun Nov 23 17:49:15 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>