| Previous changeset 16:cd7e644cae1d (2021-10-08) Next changeset 18:b94789823aad (2025-05-10) |
|
Commit message:
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 48a5b169f1ea3d98761bfeaae135a808506e6cbb |
|
modified:
macros.xml trim_galore.xml |
| b |
| diff -r cd7e644cae1d -r eefb644655a5 macros.xml --- a/macros.xml Fri Oct 08 09:57:52 2021 +0000 +++ b/macros.xml Wed Mar 05 18:50:58 2025 +0000 |
| b |
| @@ -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> |
| b |
| diff -r cd7e644cae1d -r eefb644655a5 trim_galore.xml --- a/trim_galore.xml Fri Oct 08 09:57:52 2021 +0000 +++ b/trim_galore.xml Wed Mar 05 18:50:58 2025 +0000 |
| [ |
| b'@@ -3,8 +3,8 @@\n <macros>\n <import>macros.xml</import>\n </macros>\n+ <expand macro="xrefs"/>\n <expand macro="requirements" />\n- <expand macro="xrefs"/>\n <version_command>\n trim_galore --version\n </version_command>\n@@ -291,12 +291,12 @@\n </inputs>\n \n <outputs>\n- <data format_source="input_singles" name="trimmed_reads_single" from_work_dir="input_1_trimmed.fq" label="${tool.name} on ${on_string}: trimmed reads">\n+ <data format_source="singlePaired|input_singles" default_identifier_source="singlePaired|input_singles" name="trimmed_reads_single" from_work_dir="input_1_trimmed.fq" label="${tool.name} on ${on_string}: trimmed reads">\n <filter>singlePaired[\'sPaired\'] == "single"</filter>\n <filter>trimming[\'hardtrim3\'] == \'\' and trimming[\'hardtrim5\'] == \'\'</filter>\n </data>\n \n- <data format_source="input_singles" name="hardtrim_reads_single" from_work_dir="input_1_hardtrim.fq" label="${tool.name} on ${on_string}: hard-trimmed reads">\n+ <data format_source="singlePaired|input_singles" name="hardtrim_reads_single" from_work_dir="input_1_hardtrim.fq" label="${tool.name} on ${on_string}: hard-trimmed reads">\n <filter>singlePaired[\'sPaired\'] == "single"</filter>\n <filter>trimming[\'settingsType\'] == "custom"</filter>\n <filter>trimming[\'hardtrim3\'] != \'\' or trimming[\'hardtrim5\'] != \'\'</filter>\n@@ -340,42 +340,43 @@\n </collection>\n \n \n- <data format_source="input_mate1" name="trimmed_reads_pair1" from_work_dir="input_1_val_1.fq"\n+ <data format_source="singlePaired|input_mate1" default_identifier_source="singlePaired|input_mate1" name="trimmed_reads_pair1" from_work_dir="input_1_val_1.fq"\n label="${tool.name} on ${on_string}: trimmed reads pair 1">\n <filter>singlePaired[\'sPaired\'] == "paired"</filter>\n <filter>trimming[\'hardtrim3\'] == \'\' and trimming[\'hardtrim5\'] == \'\'</filter>\n <filter>trimming[\'clock\'] == False</filter>\n </data>\n \n- <data format_source="input_mate2" name="trimmed_reads_pair2" from_work_dir="input_2_val_2.fq"\n+ <data format_source="singlePaired|input_mate2" default_identifier_source="singlePaired|input_mate2" name="trimmed_reads_pair2" from_work_dir="input_2_val_2.fq"\n label="${tool.name} on ${on_string}: trimmed reads pair 2">\n <filter>singlePaired[\'sPaired\'] == "paired"</filter>\n <filter>trimming[\'hardtrim3\'] == \'\' and trimming[\'hardtrim5\'] == \'\'</filter>\n <filter>trimming[\'clock\'] == False</filter>\n </data>\n \n- <data format_source="input_mate1" name="unpaired_reads_1" from_work_dir="input_1_unpaired_1.fq"\n+ <data format_source="singlePaired|input_mate1" default_identifier_source="singlePaired|input_mate1" name="unpaired_reads_1" from_work_dir="input_1_unpaired_1.fq"\n label="${tool.name} on ${on_string}: unpaired reads (1)">\n <filter>params[\'settingsType\'] == "custom"</filter>\n <filter>params[\'retain_unpaired\'][\'retain_unpaired_select\'] == "retain_unpaired_output"</filter>\n <filter>singlePaired[\'sPaired\'] == "paired"</filter>\n </data>\n \n- <data format_source="input_mate2" name="unpaired_reads_2" from_work_dir="input_2_unpaired_2.fq"\n+ <data format_source="singlePaired|input_mate2" default_identifier_source="singlePaired|input_mate2" name="unpaired_reads_2" from_work_dir="input_2_unpaired_2.fq"\n label="${tool.name} on ${on_string}: unpaired reads (2)">\n <filter>params[\'settingsType\'] == "custom"</filter>\n <filter>params[\'retain_unpaired\'][\'retain_unpaired_select\'] == "retain_unpaired_output"</filter>\n <filter>singlePaired[\'sPaired\'] == "paired"</filter>\n </data>\n+\n <!--Hard-trimmed paired reads-->\n- <data format_source="input_mate1" name="hardtrimmed_reads_pair1" from_work_dir="input_'..b'aired">\n+ <param name="retain_unpaired_select" value="retain_unpaired_output" />\n+ </conditional>\n+ </conditional>\n <output name="report_file" file="paired_collection_example_results3gz.txt" ftype="txt" lines_diff="25" />\n-\n <output_collection name="trimmed_reads_paired_collection" type="paired">\n <element name="forward" file="paired_collection_example_pair1_results3.fastq.gz" ftype="fastqsanger.gz" decompress="true" />\n <element name="reverse" file="paired_collection_example_pair2_results3.fastq.gz" ftype="fastqsanger.gz" decompress="true" />\n@@ -520,9 +561,11 @@\n </test>\n <!--Test hard-trim option-->\n <test expect_num_outputs="2">\n- <param name="input_mate1" value="bwa-mem-fastq1.fq" ftype="fastqsanger" />\n- <param name="input_mate2" value="bwa-mem-fastq2.fq" ftype="fastqsanger" />\n- <param name="sPaired" value="paired" />\n+ <conditional name="singlePaired">\n+ <param name="input_mate1" value="bwa-mem-fastq1.fq" ftype="fastqsanger" />\n+ <param name="input_mate2" value="bwa-mem-fastq2.fq" ftype="fastqsanger" />\n+ <param name="sPaired" value="paired" />\n+ </conditional>\n <conditional name="trimming">\n <param name="settingsType" value="custom" />\n <param name="hardtrim3" value="20"/>\n@@ -531,9 +574,11 @@\n <output name="hardtrimmed_reads_pair1" file="paired_hardtrimmed3_pair2_.fastqsanger" ftype="fastqsanger"/>\n </test>\n <test expect_num_outputs="2">\n- <param name="input_mate1" value="bwa-mem-fastq1.fq" ftype="fastqsanger" />\n- <param name="input_mate2" value="bwa-mem-fastq2.fq" ftype="fastqsanger" />\n- <param name="sPaired" value="paired" />\n+ <conditional name="singlePaired">\n+ <param name="input_mate1" value="bwa-mem-fastq1.fq" ftype="fastqsanger" />\n+ <param name="input_mate2" value="bwa-mem-fastq2.fq" ftype="fastqsanger" />\n+ <param name="sPaired" value="paired" />\n+ </conditional>\n <conditional name="trimming">\n <param name="settingsType" value="custom" />\n <param name="hardtrim5" value="20"/>\n@@ -544,9 +589,11 @@\n \n <!--Test mouse epigenetic clock option-->\n <test expect_num_outputs="2">\n- <param name="input_mate1" value="bwa-mem-fastq1.fq" ftype="fastqsanger" />\n- <param name="input_mate2" value="bwa-mem-fastq2.fq" ftype="fastqsanger" />\n- <param name="sPaired" value="paired" />\n+ <conditional name="singlePaired">\n+ <param name="input_mate1" value="bwa-mem-fastq1.fq" ftype="fastqsanger" />\n+ <param name="input_mate2" value="bwa-mem-fastq2.fq" ftype="fastqsanger" />\n+ <param name="sPaired" value="paired" />\n+ </conditional>\n <conditional name="trimming">\n <param name="settingsType" value="custom" />\n <param name="clock" value="true"/>\n@@ -556,9 +603,11 @@\n </test>\n <!--Test polyA option-->\n <test expect_num_outputs="2">\n- <param name="input_mate1" value="bwa-mem-fastq1.fq" ftype="fastqsanger" />\n- <param name="input_mate2" value="bwa-mem-fastq2.fq" ftype="fastqsanger" />\n- <param name="sPaired" value="paired" />\n+ <conditional name="singlePaired">\n+ <param name="input_mate1" value="bwa-mem-fastq1.fq" ftype="fastqsanger" />\n+ <param name="input_mate2" value="bwa-mem-fastq2.fq" ftype="fastqsanger" />\n+ <param name="sPaired" value="paired" />\n+ </conditional>\n <conditional name="trimming">\n <param name="settingsType" value="custom" />\n <param name="polyA" value="true"/>\n' |