Mercurial > repos > sanbi-uwc > confil
view confil.xml @ 12:5ec97cccb3fe draft
planemo upload for repository https://github.com/COMBAT-TB/confil commit b1a96c1b50cea70a20d4e606100879da8b6ed1b2
author | sanbi-uwc |
---|---|
date | Mon, 11 Mar 2019 07:18:34 -0400 |
parents | 72cb19a32d8b |
children | bbf9ab2ebee7 |
line wrap: on
line source
<tool id="confil" name="Contamination Filter (confil)" version="@VERSION@+galaxy0"> <macros> <token name="@VERSION@">0.1.4</token> </macros> <requirements> <requirement type="package" version="@VERSION@">confil</requirement> <requirement type="package" version="7.0">click</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ #set $input_type = $input_type_conditional.input_type #import re ####### Single Input #if $input_type == "single" ln -s "${input_type_conditional.single_input}" $input_type_conditional.single_input.element_identifier && #set report_name = os.path.splitext(os.path.basename($input_type_conditional.single_input.element_identifier))[0] #set report_name = re.sub('_[0-9]+$', '', str(report_name)) + '.tab' if confil --threads \${GALAXY_SLOTS:-1} --cutoff $cutoff $input_type_conditional.single_input.element_identifier ; then ln -sf "${input_type_conditional.single_input}" '$single_output_file' ; else touch '$single_output_file' ; fi ####### Paired Collection #elif $input_type == "paired_collection" ln -s "${input_type_conditional.collection_input.forward}" $input_type_conditional.collection_input.forward.element_identifier && ln -s "${input_type_conditional.collection_input.reverse}" $input_type_conditional.collection_input.reverse.element_identifier && #set report_name = os.path.splitext(os.path.basename($input_type_conditional.collection_input.forward.element_identifier))[0] #set report_name = re.sub('_[0-9]+$', '', str(report_name)) + '.tab' if confil --threads \${GALAXY_SLOTS:-1} --cutoff $cutoff --paired $input_type_conditional.collection_input.forward.element_identifier $input_type_conditional.collection_input.reverse.element_identifier ; then ln -sf "${input_type_conditional.collection_input.forward}" '$list_output.forward' && ln -sf "${input_type_conditional.collection_input.reverse}" '$list_output.reverse' ; else touch '$list_output.forward' && touch '$list_output.reverse' ; fi #end if && mv $report_name '$output_report' ]]> </command> <inputs> <conditional name="input_type_conditional"> <param name="input_type" type="select" label="Select Input Type"> <option value="single" selected="true">Single Dataset</option> <option value="paired_collection">Paired Collection</option> </param> <when value="single"> <param name="single_input" type="data" format="fq,fastq,fastq.gz,fastqsanger" label="Select FASTQ Dataset" help="Specify dataset with single reads" /> </when> <when value="paired_collection"> <param name="collection_input" format="fq,fastq,fastq.gz,fastqsanger" type="data_collection" collection_type="paired" label="Select Dataset Pair" help="Specify paired dataset collection containing paired reads" /> </when> </conditional> <param name="cutoff" type="integer" label="Cutoff percentage" value="90" min="50" max="99" /> </inputs> <outputs> <data name="output_report" format="tabular" label="${tool.name} on ${on_string} kraken2 report" /> <data name="single_output_file" format="fastq" label="${tool.name} on ${on_string} single output"> <filter>input_type_conditional['input_type'] == "single"</filter> </data> <collection name="list_output" type="paired" label="${tool.name} on ${on_string} paired output" structured_like="collection_input" inherit_format="true"> <filter>input_type_conditional['input_type'] == "paired_collection"</filter> <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="single_output_file" ftype="fastq" file="seq_1.fastq" /> </test> <test> <param name="collection_input"> <collection type="paired"> <element name="forward" value="seq_1.fastq" /> <element name="reverse" value="seq_2.fastq" /> </collection> </param> <param name="input_type" value="paired_collection" /> <output name="output_report" ftype='tabular' file="seq.tab" /> <output_collection name="list_output" type="paired"> <element name="forward" value="seq_1.fastq"> </element> <element name="reverse" value="seq_2.fastq"> </element> </output_collection> </test> </tests> <help><![CDATA[ confil parses a kraken2 report and determines contamination based on a specified cutoff. ]]> </help> <citations> <citation type="bibtex"> @misc{githubconfil, author = {SANBI-SA}, year = {2019}, title = {confil}, publisher = {GitHub}, journal = {GitHub repository}, url = {https://github.com/COMBAT-TB/confil}, }</citation> </citations> </tool>