Mercurial > repos > lparsons > cutadapt
changeset 29:48f587c13075 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit dea830212266690dbd20448f9a89ea7bfeee4a26"
| author | iuc |
|---|---|
| date | Thu, 10 Feb 2022 12:13:05 +0000 |
| parents | c053d4cad713 |
| children | c5e2e5902201 |
| files | cutadapt.xml macros.xml test-data/cutadapt_out1.fq.gz test-data/cutadapt_out2.fq.gz |
| diffstat | 4 files changed, 16 insertions(+), 11 deletions(-) [+] |
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--- a/cutadapt.xml Sat Nov 27 10:09:14 2021 +0000 +++ b/cutadapt.xml Thu Feb 10 12:13:05 2022 +0000 @@ -93,13 +93,8 @@ #else: @read1_options@ @read2_options@ - #if $library.type == "paired" - --output='$out1' - --paired-output='$out2' - #else - --output='$out_pairs.forward' - --paired-output='$out_pairs.reverse' - #end if + --output='$out1' + --paired-output='$out2' #end if --error-rate=$adapter_options.error_rate @@ -337,6 +332,8 @@ <collection name="out_pairs" type="paired" format_source="input_1" label="${tool.name} on ${on_string}: Reads"> <filter>library['type'] == 'paired_collection' and 'multiple_output' not in output_selector</filter> + <data name="forward" from_work_dir="out1.fq*" /> + <data name="reverse" from_work_dir="out2.fq*" /> </collection> <data name="report" format="txt" from_work_dir="report.txt" label="${tool.name} on ${on_string}: Report"> @@ -478,9 +475,17 @@ </conditional> </repeat> </section> - <output_collection name="out_pairs" type="paired"> - <element name="forward" decompress="True" file="cutadapt_out1.fq.gz" ftype="fastq.gz" /> - <element name="reverse" decompress="True" file="cutadapt_out2.fq.gz" ftype="fastq.gz" /> + <output_collection name="out_pairs" type="paired" count="2"> + <element name="forward" decompress="true" file="cutadapt_out1.fq.gz" ftype="fastq.gz"> + <assert_contents> + <has_size value="12000" delta="2000" /> + </assert_contents> + </element> + <element name="reverse" decompress="true" file="cutadapt_out2.fq.gz" ftype="fastq.gz"> + <assert_contents> + <has_size value="12000" delta="2000" /> + </assert_contents> + </element> </output_collection> </test> <!-- Ensure built-in adapters work -->
--- a/macros.xml Sat Nov 27 10:09:14 2021 +0000 +++ b/macros.xml Thu Feb 10 12:13:05 2022 +0000 @@ -1,6 +1,6 @@ <macros> <token name="@TOOL_VERSION@">3.5</token> - <token name="@VERSION_SUFFIX@">1</token> + <token name="@VERSION_SUFFIX@">2</token> <token name="@FASTQ_TYPES@">fastq.gz,fastq,fasta</token> <xml name="edam_ontology"> <edam_topics>