Mercurial > repos > sanbi-uwc > confil
changeset 5:a7b05dd0087d draft
planemo upload for repository https://github.com/COMBAT-TB/confil commit 83c5a4f7379a73750c815756a4e84af8ecabe78b-dirty
author | sanbi-uwc |
---|---|
date | Mon, 04 Mar 2019 07:42:05 -0500 |
parents | eaf51f9aff10 |
children | 2b90d0574ea5 |
files | confil.xml |
diffstat | 1 files changed, 17 insertions(+), 10 deletions(-) [+] |
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--- a/confil.xml Mon Mar 04 03:28:57 2019 -0500 +++ b/confil.xml Mon Mar 04 07:42:05 2019 -0500 @@ -15,7 +15,7 @@ python $__tool_directory__/confil/confil.py --threads $threads --cutoff $cutoff $input_type_conditional.single_input.element_identifier && mv $report_name '$output_report' - && ln -sf "${input_type_conditional.single_input}" '$output_file1' + && ln -sf "${input_type_conditional.single_input}" '$single_output_file' ####### Paired Collection #elif $input_type == "paired_collection" @@ -27,8 +27,8 @@ python $__tool_directory__/confil/confil.py --threads $threads --cutoff $cutoff --paired $input_type_conditional.collection_input.forward.element_identifier $input_type_conditional.collection_input.reverse.element_identifier && mv $report_name '$output_report' - && ln -sf "${input_type_conditional.collection_input.forward}" '$output_file1' - && ln -sf "${input_type_conditional.collection_input.reverse}" '$output_file2' + && ln -sf "${input_type_conditional.collection_input.forward}" '$list_output.forward' + && ln -sf "${input_type_conditional.collection_input.reverse}" '$list_output.reverse' #end if ]]> </command> @@ -49,19 +49,22 @@ <param name="threads" type="integer" label="Number of threads" value="1" min="1" max="4" /> </inputs> <outputs> - <data name="output_report" format="tabular" label="${tool.name} report" /> - <data name="output_file1" format="fastq" label="${tool.name} report"> + <data name="output_report" format="tabular" label="Kraken2 report" /> + <data name="single_output_file" format="fastq" label="${tool.name} single output"> + <filter>input_type_conditional['input_type'] == "single"</filter> </data> - <data name="output_file2" format="fastq" label="${tool.name} report"> + <collection name="list_output" type="paired" label="${tool.name} paired output" structured_like="collection_input" inherit_format="true"> <filter>input_type_conditional['input_type'] == "paired_collection"</filter> - </data> + <data name="forward" format="fastq" /> + <data name="reverse" format="fastq" /> + </collection> </outputs> <tests> <test> <param name="single_input" value="seq_1.fastq" /> <param name="input_type" value="single" /> <output name="output_report" ftype="tabular" file="seq.tab" /> - <output name="output_file1" ftype="fastq" file="seq_1.fastq" /> + <output name="single_output_file" ftype="fastq" file="seq_1.fastq" /> </test> <test> <param name="collection_input"> @@ -72,8 +75,12 @@ </param> <param name="input_type" value="paired_collection" /> <output name="output_report" ftype='tabular' file="seq.tab" /> - <output name="output_file1" ftype='fastq' file="seq_1.fastq" /> - <output name="output_file2" ftype='fastq' file="seq_2.fastq" /> + <output_collection name="list_output" type="paired"> + <element name="forward"> + </element> + <element name="reverse"> + </element> + </output_collection> </test> </tests> <help><![CDATA[