| Previous changeset 16:9a38087e3bfd (2024-01-14) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/packages/trimmomatic commit 6151dc895107d028c525362fb16b91388e10f2f2 |
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modified:
trimmomatic.xml trimmomatic_macros.xml |
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| diff -r 9a38087e3bfd -r b9aaed85cbd1 trimmomatic.xml --- a/trimmomatic.xml Sun Jan 14 11:00:33 2024 +0000 +++ b/trimmomatic.xml Wed Jan 24 08:56:01 2024 +0000 |
| [ |
| @@ -120,15 +120,15 @@ <option value="pair_of_files">Paired-end (two separate input files)</option> <option value="collection">Paired-end (as collection)</option> </param> - <when value="se"> - <param name="fastq_in" type="data" format="fastqsanger,fastqsanger.gz,fastqillumina,fastqillumina.gz,fastqsolexa,fastqsolexa.gz" label="Input FASTQ file" /> - </when> - <when value="pair_of_files"> - <param name="fastq_r1_in" type="data" format="fastqsanger,fastqsanger.gz,fastqillumina,fastqillumina.gz,fastqsolexa,fastqsolexa.gz" - label="Input FASTQ file (R1/first of pair)" /> - <param name="fastq_r2_in" type="data" format="fastqsanger,fastqsanger.gz,fastqillumina,fastqillumina.gz,fastqsolexa,fastqsolexa.gz" - label="Input FASTQ file (R2/second of pair)" /> - </when> + <when value="se"> + <param name="fastq_in" type="data" format="fastqsanger,fastqsanger.gz,fastqillumina,fastqillumina.gz,fastqsolexa,fastqsolexa.gz" label="Input FASTQ file" /> + </when> + <when value="pair_of_files"> + <param name="fastq_r1_in" type="data" format="fastqsanger,fastqsanger.gz,fastqillumina,fastqillumina.gz,fastqsolexa,fastqsolexa.gz" + label="Input FASTQ file (R1/first of pair)" /> + <param name="fastq_r2_in" type="data" format="fastqsanger,fastqsanger.gz,fastqillumina,fastqillumina.gz,fastqsolexa,fastqsolexa.gz" + label="Input FASTQ file (R2/second of pair)" /> + </when> <when value="collection"> <param name="fastq_pair" format="fastqsanger,fastqsanger.gz,fastqillumina,fastqillumina.gz,fastqsolexa,fastqsolexa.gz" type="data_collection" collection_type="paired" label="Select FASTQ dataset collection with R1/R2 pair" /> </when> @@ -222,19 +222,19 @@ <param name="output_err" type="boolean" label="Output trimmomatic log messages?" truevalue="yes" falsevalue="no" checked="False" help="these are the messages written to stderr (eg. for use in MultiQC)" /> </inputs> <outputs> - <data name="fastq_out_r1_paired" label="${tool.name} on ${readtype.fastq_r1_in.name} (R1 paired)" format_source="fastq_r1_in"> + <data name="fastq_out_r1_paired" default_identifier_source="readtype|fastq_r1_in" label="${tool.name} on ${readtype.fastq_r1_in.name} (R1 paired)" format_source="fastq_r1_in"> <filter>readtype['single_or_paired'] == "pair_of_files"</filter> </data> - <data name="fastq_out_r2_paired" label="${tool.name} on ${readtype.fastq_r2_in.name} (R2 paired)" format_source="fastq_r2_in"> + <data name="fastq_out_r2_paired" default_identifier_source="readtype|fastq_r2_in" label="${tool.name} on ${readtype.fastq_r2_in.name} (R2 paired)" format_source="fastq_r2_in"> <filter>readtype['single_or_paired'] == "pair_of_files"</filter> </data> - <data name="fastq_out_r1_unpaired" label="${tool.name} on ${readtype.fastq_r1_in.name} (R1 unpaired)" format_source="fastq_r1_in"> + <data name="fastq_out_r1_unpaired" default_identifier_source="readtype|fastq_r1_in" label="${tool.name} on ${readtype.fastq_r1_in.name} (R1 unpaired)" format_source="fastq_r1_in"> <filter>readtype['single_or_paired'] == "pair_of_files"</filter> </data> - <data name="fastq_out_r2_unpaired" label="${tool.name} on ${readtype.fastq_r2_in.name} (R2 unpaired)" format_source="fastq_r2_in"> + <data name="fastq_out_r2_unpaired" default_identifier_source="readtype|fastq_r2_in" label="${tool.name} on ${readtype.fastq_r2_in.name} (R2 unpaired)" format_source="fastq_r2_in"> <filter>readtype['single_or_paired'] == "pair_of_files"</filter> </data> - <data name="fastq_out" label="${tool.name} on ${readtype.fastq_in.name}" format_source="fastq_in"> + <data name="fastq_out" default_identifier_source="readtype|fastq_in" label="${tool.name} on ${readtype.fastq_in.name}" format_source="fastq_in"> <filter>readtype['single_or_paired'] == 'se'</filter> </data> <collection name="fastq_out_paired" type="paired" label="${tool.name} on ${on_string}: paired"> @@ -242,10 +242,10 @@ <data name="forward" label="${tool.name} on ${readtype.fastq_pair.forward.name} (R1 paired)" format_source="fastq_pair['forward']"/> <data name="reverse" label="${tool.name} on ${readtype.fastq_pair.reverse.name} (R2 paired)" format_source="fastq_pair['reverse']"/> </collection> - <collection name="fastq_out_unpaired" type="paired" label="${tool.name} on ${on_string}: unpaired"> - <filter>readtype['single_or_paired'] == "collection"</filter> - <data name="forward" label="${tool.name} on ${readtype.fastq_pair.forward.name} (R1 unpaired)" format_source="fastq_pair['forward']"/> - <data name="reverse" label="${tool.name} on ${readtype.fastq_pair.reverse.name} (R2 unpaired)" format_source="fastq_pair['reverse']"/> + <collection name="fastq_out_unpaired" type="paired" label="${tool.name} on ${on_string}: unpaired"> + <filter>readtype['single_or_paired'] == "collection"</filter> + <data name="forward" label="${tool.name} on ${readtype.fastq_pair.forward.name} (R1 unpaired)" format_source="fastq_pair['forward']"/> + <data name="reverse" label="${tool.name} on ${readtype.fastq_pair.reverse.name} (R2 unpaired)" format_source="fastq_pair['reverse']"/> </collection> <data name="log_file" format="txt" label="${tool.name} on ${on_string} (trimlog file)" from_work_dir="trimlog"> <filter>output_logs</filter> |
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| diff -r 9a38087e3bfd -r b9aaed85cbd1 trimmomatic_macros.xml --- a/trimmomatic_macros.xml Sun Jan 14 11:00:33 2024 +0000 +++ b/trimmomatic_macros.xml Wed Jan 24 08:56:01 2024 +0000 |
| [ |
| @@ -6,5 +6,5 @@ <token name="@CONDA_TRIMMOMATIC_JAR_PATH@">if [ -z "\$TRIMMOMATIC_JAR_PATH" ]; then export TRIMMOMATIC_JAR_PATH=\$(dirname \$(readlink -e \$(which trimmomatic))); fi</token> <token name="@CONDA_TRIMMOMATIC_ADAPTERS_PATH@">if [ -z "\$TRIMMOMATIC_ADAPTERS_PATH" ]; then export TRIMMOMATIC_ADAPTERS_PATH=\$(dirname \$(readlink -e \$(which trimmomatic)))/adapters; fi</token> <token name="@TOOL_VERSION@">0.39</token> - <token name="@VERSION_SUFFIX@">1</token> + <token name="@VERSION_SUFFIX@">2</token> </macros> |