Mercurial > repos > lparsons > cutadapt
changeset 18:5c7e7d905b33 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b58d6ff959a1d920fd0d9b02e43d2482667d61e8
author | iuc |
---|---|
date | Thu, 13 Dec 2018 20:54:04 -0500 (2018-12-14) |
parents | 52ef1be47553 |
children | 49370cb85f0f |
files | cutadapt.xml test-data/A1.fastq.gz test-data/A2.fastq.gz test-data/cutadapt_in_split.fastq.gz test-data/unknown.fastq.gz |
diffstat | 5 files changed, 39 insertions(+), 9 deletions(-) [+] |
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--- a/cutadapt.xml Fri Nov 09 11:33:40 2018 -0500 +++ b/cutadapt.xml Thu Dec 13 20:54:04 2018 -0500 @@ -82,7 +82,7 @@ #if str( $library.type ) == "single": @read1_options@ #if $output_options.multiple_output: - --output='split/{name}.fastq' + --output='split/{name}.${input_1.ext}' #else: --output='$out1' #end if @@ -236,6 +236,7 @@ <outputs> <data name="out1" format="fastqsanger" metadata_source="input_1" from_work_dir="out1*" label="${tool.name} on ${on_string}: Read 1 Output"> + <filter>(output_options['multiple_output'] is False)</filter> <expand macro="inherit_format_1" /> </data> <data name="out2" format="fastqsanger" metadata_source="input_2" from_work_dir="out2*" label="${tool.name} on ${on_string}: Read 2 Output" > @@ -290,8 +291,8 @@ <expand macro="inherit_format_2" /> </data> - <collection name="split_output" type="list" format_source="input" label="${tool.name} on ${on_string}: Split outputs"> - <discover_datasets pattern="__designation_and_ext__" directory="split" visible="false" /> + <collection name="split_output" type="list" label="${tool.name} on ${on_string}: Split outputs" > + <discover_datasets pattern="(?P<designation>.+)\.(?P<ext>fastq.*)" directory="split" /> <filter>(output_options['multiple_output'] is True)</filter> </collection> @@ -422,7 +423,7 @@ </repeat> </section> </conditional> - <param name="report" value="True" /> + <param name="report" value="False" /> <param name="info_file" value="False" /> <param name="multiple_output" value="True" /> <output_collection name="split_output" type="list" count="3"> @@ -433,14 +434,43 @@ <element name="unknown" value="unknown.fastq" ftype="fastq"> </element> </output_collection> - <output name="report"> - <assert_contents> - <has_text text="Summary"/> - </assert_contents> - </output> </test> + <test> + <conditional name="library"> + <param name="type" value="single" /> + <param name="input_1" ftype="fastq.gz" value="cutadapt_in_split.fastq.gz" /> + <section name="r1" > + <repeat name="front_adapters"> + <conditional name="front_adapter_source"> + <param name="front_adapter_source_list" value="user"/> + <param name="front_adapter_name" value="A1" /> + <param name="front_adapter" value="^GTCGGTAA" /> + </conditional> + </repeat> + <repeat name="front_adapters"> + <conditional name="front_adapter_source"> + <param name="front_adapter_source_list" value="user"/> + <param name="front_adapter_name" value="A2" /> + <param name="front_adapter" value="^AGGTCACT" /> + </conditional> + </repeat> + </section> + </conditional> + <param name="report" value="False" /> + <param name="info_file" value="False" /> + <param name="multiple_output" value="True" /> + <output_collection name="split_output" type="list" count="3"> + <element name="A1" decompress="True" file="A1.fastq.gz" ftype="fastq.gz"> + </element> + <element name="A2" decompress="True" file="A2.fastq.gz" ftype="fastq.gz"> + </element> + <element name="unknown" decompress="True" file="unknown.fastq.gz" ftype="fastq.gz"> + </element> + </output_collection> + </test> + </tests> <help><![CDATA[