Mercurial > repos > bgruening > trim_galore

changeset 17:eefb644655a5 draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 48a5b169f1ea3d98761bfeaae135a808506e6cbb
author bgruening
date Wed, 05 Mar 2025 18:50:58 +0000 (16 hours ago)
parents cd7e644cae1d
children
files macros.xml trim_galore.xml
diffstat 2 files changed, 129 insertions(+), 80 deletions(-) [+]
line wrap: on
line diff
--- a/macros.xml	Fri Oct 08 09:57:52 2021 +0000
+++ b/macros.xml	Wed Mar 05 18:50:58 2025 +0000
@@ -1,6 +1,6 @@
 <macros>
     <token name="@TOOL_VERSION@">0.6.7</token>
-    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@VERSION_SUFFIX@">1</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">trim-galore</requirement>
--- a/trim_galore.xml	Fri Oct 08 09:57:52 2021 +0000
+++ b/trim_galore.xml	Wed Mar 05 18:50:58 2025 +0000
@@ -3,8 +3,8 @@
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="xrefs"/>
     <expand macro="requirements" />
-    <expand macro="xrefs"/>
     <version_command>
         trim_galore --version
     </version_command>
@@ -291,12 +291,12 @@
     </inputs>
 
     <outputs>
-        <data format_source="input_singles" name="trimmed_reads_single" from_work_dir="input_1_trimmed.fq" label="${tool.name} on ${on_string}: trimmed reads">
+        <data format_source="singlePaired|input_singles" default_identifier_source="singlePaired|input_singles" name="trimmed_reads_single" from_work_dir="input_1_trimmed.fq" label="${tool.name} on ${on_string}: trimmed reads">
             <filter>singlePaired['sPaired'] == "single"</filter>
             <filter>trimming['hardtrim3'] == '' and trimming['hardtrim5'] == ''</filter>
         </data>
 
-        <data format_source="input_singles" name="hardtrim_reads_single" from_work_dir="input_1_hardtrim.fq" label="${tool.name} on ${on_string}: hard-trimmed reads">
+        <data format_source="singlePaired|input_singles" name="hardtrim_reads_single" from_work_dir="input_1_hardtrim.fq" label="${tool.name} on ${on_string}: hard-trimmed reads">
             <filter>singlePaired['sPaired'] == "single"</filter>
             <filter>trimming['settingsType'] == "custom"</filter>
             <filter>trimming['hardtrim3'] != '' or trimming['hardtrim5'] != ''</filter>
@@ -340,42 +340,43 @@
         </collection>
 
 
-        <data format_source="input_mate1" name="trimmed_reads_pair1" from_work_dir="input_1_val_1.fq"
+        <data format_source="singlePaired|input_mate1" default_identifier_source="singlePaired|input_mate1" name="trimmed_reads_pair1" from_work_dir="input_1_val_1.fq"
             label="${tool.name} on ${on_string}: trimmed reads pair 1">
             <filter>singlePaired['sPaired'] == "paired"</filter>
             <filter>trimming['hardtrim3'] == '' and trimming['hardtrim5'] == ''</filter>
             <filter>trimming['clock'] == False</filter>
         </data>
 
-        <data format_source="input_mate2" name="trimmed_reads_pair2" from_work_dir="input_2_val_2.fq"
+        <data format_source="singlePaired|input_mate2" default_identifier_source="singlePaired|input_mate2" name="trimmed_reads_pair2" from_work_dir="input_2_val_2.fq"
             label="${tool.name} on ${on_string}: trimmed reads pair 2">
             <filter>singlePaired['sPaired'] == "paired"</filter>
             <filter>trimming['hardtrim3'] == '' and trimming['hardtrim5'] == ''</filter>
             <filter>trimming['clock'] == False</filter>
         </data>
 
-        <data format_source="input_mate1" name="unpaired_reads_1" from_work_dir="input_1_unpaired_1.fq"
+        <data format_source="singlePaired|input_mate1" default_identifier_source="singlePaired|input_mate1" name="unpaired_reads_1" from_work_dir="input_1_unpaired_1.fq"
             label="${tool.name} on ${on_string}: unpaired reads (1)">
             <filter>params['settingsType'] == "custom"</filter>
             <filter>params['retain_unpaired']['retain_unpaired_select'] == "retain_unpaired_output"</filter>
             <filter>singlePaired['sPaired'] == "paired"</filter>
         </data>
 
-        <data format_source="input_mate2" name="unpaired_reads_2" from_work_dir="input_2_unpaired_2.fq"
+        <data format_source="singlePaired|input_mate2" default_identifier_source="singlePaired|input_mate2" name="unpaired_reads_2" from_work_dir="input_2_unpaired_2.fq"
             label="${tool.name} on ${on_string}: unpaired reads (2)">
             <filter>params['settingsType'] == "custom"</filter>
             <filter>params['retain_unpaired']['retain_unpaired_select'] == "retain_unpaired_output"</filter>
             <filter>singlePaired['sPaired'] == "paired"</filter>
         </data>
+
         <!--Hard-trimmed paired reads-->
-        <data format_source="input_mate1" name="hardtrimmed_reads_pair1" from_work_dir="input_1_hardtrim.fq"
+        <data format_source="singlePaired|input_mate1" default_identifier_source="singlePaired|input_mate1" name="hardtrimmed_reads_pair1" from_work_dir="input_1_hardtrim.fq"
             label="${tool.name} on ${on_string}: hard-trimmed reads pair 1">
             <filter>singlePaired['sPaired'] == "paired"</filter>
             <filter>trimming['settingsType'] == 'custom'</filter>
             <filter>trimming['hardtrim3'] or trimming['hardtrim5']</filter>
         </data>
 
-        <data format_source="input_mate2" name="hardtrimmed_reads_pair2" from_work_dir="input_2_hardtrim.fq"
+        <data format_source="singlePaired|input_mate2" default_identifier_source="singlePaired|input_mate2" name="hardtrimmed_reads_pair2" from_work_dir="input_2_hardtrim.fq"
             label="${tool.name} on ${on_string}: hard-trimmed reads pair 2">
             <filter>singlePaired['sPaired'] == "paired"</filter>
             <filter>trimming['settingsType'] == 'custom'</filter>
@@ -383,14 +384,14 @@
         </data>
 
         <!--Mouse epigenetic mode paired reads-->
-        <data format_source="input_mate1" name="mec_reads_pair1" from_work_dir="input_1.clock_UMI.R1.fq"
+        <data format_source="singlePaired|input_mate1" default_identifier_source="singlePaired|input_mate1" name="mec_reads_pair1" from_work_dir="input_1.clock_UMI.R1.fq"
             label="${tool.name} on ${on_string}: MEC reads pair 1">
             <filter>singlePaired['sPaired'] == "paired"</filter>
             <filter>trimming['settingsType'] == 'custom'</filter>
             <filter>trimming['clock']</filter>
         </data>
 
-        <data format_source="input_mate2" name="mec_reads_pair2" from_work_dir="input_2.clock_UMI.R2.fq"
+        <data format_source="singlePaired|input_mate2" default_identifier_source="singlePaired|input_mate2" name="mec_reads_pair2" from_work_dir="input_2.clock_UMI.R2.fq"
             label="${tool.name} on ${on_string}: MEC reads pair 2">
             <filter>singlePaired['sPaired'] == "paired"</filter>
             <filter>trimming['settingsType'] == 'custom'</filter>
@@ -405,84 +406,121 @@
 
     <tests>
         <test expect_num_outputs="2">
-            <param name="input_singles" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
-            <param name="sPaired" value="single" />
-            <param name="settingsType" value="custom" />
-            <param name="report" value="true" />
+            <conditional name="singlePaired">
+                <param name="input_singles" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
+                <param name="sPaired" value="single" />
+            </conditional>
+            <conditional name="params">
+                <param name="settingsType" value="custom" />
+                <param name="report" value="true" />
+            </conditional>
             <output name="trimmed_reads_single" file="sanger_full_range_results1.fastqsanger" ftype="fastqsanger"/>
             <output name="report_file" file="sanger_full_range_report_results1.txt" ftype="txt" lines_diff="12" />
         </test>
         <test expect_num_outputs="2">
-            <param name="input_singles" value="sanger_full_range_original_sanger.fastq.gz" ftype="fastqsanger.gz" />
-            <param name="sPaired" value="single" />
-            <param name="settingsType" value="custom" />
-            <param name="report" value="true" />
+            <conditional name="singlePaired">
+                <param name="input_singles" value="sanger_full_range_original_sanger.fastq.gz" ftype="fastqsanger.gz" />
+                <param name="sPaired" value="single" />
+            </conditional>
+            <conditional name="params">
+                <param name="settingsType" value="custom" />
+                <param name="report" value="true" />
+            </conditional>
             <output name="trimmed_reads_single" file="sanger_full_range_results1.fastq.gz" ftype="fastqsanger.gz" decompress="true" />
             <output name="report_file" file="sanger_full_range_report_results1gz.txt" ftype="txt" lines_diff="12" />
         </test>
 
         <test expect_num_outputs="1">
-            <param name="input_singles" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
-            <param name="sPaired" value="single" />
-            <param name="trimming_select" value="--illumina" />
+            <conditional name="singlePaired">
+                <param name="input_singles" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
+                <param name="sPaired" value="single" />
+                <conditional name="trimming">
+                    <param name="trimming_select" value="--illumina" />
+                </conditional>
+            </conditional>
             <output name="trimmed_reads_single" file="sanger_full_range_results2.fastqsanger" ftype="fastqsanger"/>
         </test>
         <test expect_num_outputs="1">
-            <param name="input_singles" value="sanger_full_range_original_sanger.fastq.gz" ftype="fastqsanger.gz" />
-            <param name="sPaired" value="single" />
-            <param name="trimming_select" value="--illumina" />
+            <conditional name="singlePaired">
+                <param name="input_singles" value="sanger_full_range_original_sanger.fastq.gz" ftype="fastqsanger.gz" />
+                <param name="sPaired" value="single" />
+                <conditional name="trimming">
+                    <param name="trimming_select" value="--illumina" />
+                </conditional>
+            </conditional>
             <output name="trimmed_reads_single" file="sanger_full_range_results2.fastq.gz" ftype="fastqsanger.gz" decompress="true" />
         </test>
 
         <test expect_num_outputs="1">
-            <param name="input_singles" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
-            <param name="sPaired" value="single" />
-            <param name="adapter" value="AAAGAGC" />
+            <conditional name="singlePaired">
+                <param name="input_singles" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
+                <param name="sPaired" value="single" />
+                <conditional name="trimming">
+                    <param name="trimming_select" value="user" />
+                    <param name="adapter" value="AAAGAGC" />
+                </conditional>
+            </conditional>
             <output name="trimmed_reads_single" file="sanger_full_range_results3.fastqsanger" ftype="fastqsanger"/>
         </test>
         <test expect_num_outputs="1">
-            <param name="input_singles" value="sanger_full_range_original_sanger.fastq.gz" ftype="fastqsanger.gz" />
-            <param name="sPaired" value="single" />
-            <param name="adapter" value="AAAGAGC" />
+            <conditional name="singlePaired">
+                <param name="input_singles" value="sanger_full_range_original_sanger.fastq.gz" ftype="fastqsanger.gz" />
+                <param name="sPaired" value="single" />
+                <conditional name="trimming">
+                    <param name="trimming_select" value="user" />
+                    <param name="adapter" value="AAAGAGC" />
+                </conditional>
+            </conditional>
             <output name="trimmed_reads_single" file="sanger_full_range_results3.fastq.gz" ftype="fastqsanger.gz" decompress="true" />
         </test>
 
         <test expect_num_outputs="3">
-            <param name="input_mate1" value="bwa-mem-fastq1.fq" ftype="fastqsanger" />
-            <param name="input_mate2" value="bwa-mem-fastq2.fq" ftype="fastqsanger" />
-            <param name="sPaired" value="paired" />
-            <param name="settingsType" value="custom" />
-            <param name="report" value="true" />
+            <conditional name="singlePaired">
+                <param name="input_mate1" value="bwa-mem-fastq1.fq" ftype="fastqsanger" />
+                <param name="input_mate2" value="bwa-mem-fastq2.fq" ftype="fastqsanger" />
+                <param name="sPaired" value="paired" />
+            </conditional>
+            <conditional name="params">
+                <param name="settingsType" value="custom" />
+                <param name="report" value="true" />
+            </conditional>
             <output name="trimmed_reads_pair1" file="paired_example_pair1_results2.fastqsanger" ftype="fastqsanger"/>
             <output name="trimmed_reads_pair2" file="paired_example_pair2_results2.fastqsanger" ftype="fastqsanger"/>
             <output name="report_file" file="paired_example_results2.txt" ftype="txt" lines_diff="24" />
         </test>
         <test expect_num_outputs="3">
-            <param name="input_mate1" value="bwa-mem-fastq1.fq.gz" ftype="fastqsanger.gz" />
-            <param name="input_mate2" value="bwa-mem-fastq2.fq.gz" ftype="fastqsanger.gz" />
-            <param name="sPaired" value="paired" />
-            <param name="settingsType" value="custom" />
-            <param name="report" value="true" />
+            <conditional name="singlePaired">
+                <param name="input_mate1" value="bwa-mem-fastq1.fq.gz" ftype="fastqsanger.gz" />
+                <param name="input_mate2" value="bwa-mem-fastq2.fq.gz" ftype="fastqsanger.gz" />
+                <param name="sPaired" value="paired" />
+            </conditional>
+            <conditional name="params">
+                <param name="settingsType" value="custom" />
+                <param name="report" value="true" />
+            </conditional>
             <output name="trimmed_reads_pair1" file="paired_example_pair1_results2.fastq.gz" ftype="fastqsanger.gz" decompress="true" />
             <output name="trimmed_reads_pair2" file="paired_example_pair2_results2.fastq.gz" ftype="fastqsanger.gz" decompress="true" />
             <output name="report_file" file="paired_example_results2gz.txt" ftype="txt" lines_diff="24" />
         </test>
 
         <test expect_num_outputs="7">
-            <param name="input_mate_pairs">
-                <collection type="paired">
-                    <element name="forward" value="bwa-mem-fastq1.fq" ftype="fastqsanger" />
-                    <element name="reverse" value="bwa-mem-fastq2.fq" ftype="fastqsanger" />
-                </collection>
-            </param>
-
-            <param name="sPaired" value="paired_collection" />
-            <param name="settingsType" value="custom" />
-            <param name="report" value="true" />
-            <param name="retain_unpaired_select" value="retain_unpaired_output" />
-
+            <conditional name="singlePaired">
+                <param name="input_mate_pairs">
+                    <collection type="paired">
+                        <element name="forward" value="bwa-mem-fastq1.fq" ftype="fastqsanger" />
+                        <element name="reverse" value="bwa-mem-fastq2.fq" ftype="fastqsanger" />
+                    </collection>
+                </param>
+                <param name="sPaired" value="paired_collection" />
+            </conditional>
+            <conditional name="params">
+                <param name="settingsType" value="custom" />
+                <param name="report" value="true" />
+                <conditional name="retain_unpaired">
+                    <param name="retain_unpaired_select" value="retain_unpaired_output" />
+                </conditional>
+            </conditional>
             <output name="report_file" file="paired_collection_example_results3.txt" ftype="txt" lines_diff="24" />
-
             <output_collection name="trimmed_reads_paired_collection" type="paired">
                 <element name="forward" file="paired_collection_example_pair1_results3.fastqsanger" ftype="fastqsanger"/>
                 <element name="reverse" file="paired_collection_example_pair2_results3.fastqsanger" ftype="fastqsanger"/>
@@ -494,20 +532,23 @@
             </output_collection>
         </test>
         <test expect_num_outputs="7">
-            <param name="input_mate_pairs">
-                <collection type="paired">
-                    <element name="forward" value="bwa-mem-fastq1.fq.gz" ftype="fastqsanger.gz" />
-                    <element name="reverse" value="bwa-mem-fastq2.fq.gz" ftype="fastqsanger.gz" />
-                </collection>
-            </param>
-
-            <param name="sPaired" value="paired_collection" />
-            <param name="settingsType" value="custom" />
-            <param name="report" value="true" />
-            <param name="retain_unpaired_select" value="retain_unpaired_output" />
-
+            <conditional name="singlePaired">
+                <param name="input_mate_pairs">
+                    <collection type="paired">
+                        <element name="forward" value="bwa-mem-fastq1.fq.gz" ftype="fastqsanger.gz" />
+                        <element name="reverse" value="bwa-mem-fastq2.fq.gz" ftype="fastqsanger.gz" />
+                    </collection>
+                </param>
+                <param name="sPaired" value="paired_collection" />
+            </conditional>
+            <conditional name="params">
+                <param name="settingsType" value="custom" />
+                <param name="report" value="true" />
+                <conditional name="retain_unpaired">
+                    <param name="retain_unpaired_select" value="retain_unpaired_output" />
+                </conditional>
+            </conditional>
             <output name="report_file" file="paired_collection_example_results3gz.txt" ftype="txt" lines_diff="25" />
-
             <output_collection name="trimmed_reads_paired_collection" type="paired">
                 <element name="forward" file="paired_collection_example_pair1_results3.fastq.gz" ftype="fastqsanger.gz" decompress="true" />
                 <element name="reverse" file="paired_collection_example_pair2_results3.fastq.gz" ftype="fastqsanger.gz" decompress="true" />
@@ -520,9 +561,11 @@
         </test>
         <!--Test hard-trim option-->
         <test expect_num_outputs="2">
-            <param name="input_mate1" value="bwa-mem-fastq1.fq" ftype="fastqsanger" />
-            <param name="input_mate2" value="bwa-mem-fastq2.fq" ftype="fastqsanger" />
-            <param name="sPaired" value="paired" />
+            <conditional name="singlePaired">
+                <param name="input_mate1" value="bwa-mem-fastq1.fq" ftype="fastqsanger" />
+                <param name="input_mate2" value="bwa-mem-fastq2.fq" ftype="fastqsanger" />
+                <param name="sPaired" value="paired" />
+            </conditional>
             <conditional name="trimming">
                 <param name="settingsType" value="custom" />
                 <param name="hardtrim3" value="20"/>
@@ -531,9 +574,11 @@
             <output name="hardtrimmed_reads_pair1" file="paired_hardtrimmed3_pair2_.fastqsanger" ftype="fastqsanger"/>
         </test>
         <test expect_num_outputs="2">
-            <param name="input_mate1" value="bwa-mem-fastq1.fq" ftype="fastqsanger" />
-            <param name="input_mate2" value="bwa-mem-fastq2.fq" ftype="fastqsanger" />
-            <param name="sPaired" value="paired" />
+            <conditional name="singlePaired">
+                <param name="input_mate1" value="bwa-mem-fastq1.fq" ftype="fastqsanger" />
+                <param name="input_mate2" value="bwa-mem-fastq2.fq" ftype="fastqsanger" />
+                <param name="sPaired" value="paired" />
+            </conditional>
             <conditional name="trimming">
                 <param name="settingsType" value="custom" />
                 <param name="hardtrim5" value="20"/>
@@ -544,9 +589,11 @@
 
         <!--Test mouse epigenetic clock option-->
         <test expect_num_outputs="2">
-            <param name="input_mate1" value="bwa-mem-fastq1.fq" ftype="fastqsanger" />
-            <param name="input_mate2" value="bwa-mem-fastq2.fq" ftype="fastqsanger" />
-            <param name="sPaired" value="paired" />
+            <conditional name="singlePaired">
+                <param name="input_mate1" value="bwa-mem-fastq1.fq" ftype="fastqsanger" />
+                <param name="input_mate2" value="bwa-mem-fastq2.fq" ftype="fastqsanger" />
+                <param name="sPaired" value="paired" />
+            </conditional>
             <conditional name="trimming">
                 <param name="settingsType" value="custom" />
                 <param name="clock" value="true"/>
@@ -556,9 +603,11 @@
         </test>
         <!--Test polyA option-->
         <test expect_num_outputs="2">
-            <param name="input_mate1" value="bwa-mem-fastq1.fq" ftype="fastqsanger" />
-            <param name="input_mate2" value="bwa-mem-fastq2.fq" ftype="fastqsanger" />
-            <param name="sPaired" value="paired" />
+            <conditional name="singlePaired">
+                <param name="input_mate1" value="bwa-mem-fastq1.fq" ftype="fastqsanger" />
+                <param name="input_mate2" value="bwa-mem-fastq2.fq" ftype="fastqsanger" />
+                <param name="sPaired" value="paired" />
+            </conditional>
             <conditional name="trimming">
                 <param name="settingsType" value="custom" />
                 <param name="polyA" value="true"/>