jpayne@3: <tool id="confindr" name="ConFindr" version="0.1.0">
jpayne@0:     <requirements>
jpayne@0:         <requirement type="package" version="0.7.4">confindr</requirement>
jpayne@0:     </requirements>
jpayne@0:     <command detect_errors="exit_code"><![CDATA[
jpayne@2:         ## Copy and optionally uncompress reads ##
jpayne@0:         #if $reads.reads_select == 'collection'
jpayne@0:             #set forward=$reads.coll.forward
jpayne@0:             #set reverse=$reads.coll.reverse
jpayne@0:             #set name=$reads.coll.name.replace(' ', '_')
jpayne@0:         #else
jpayne@0:             #set name=$forward.name.split('_')[0]
jpayne@0:         #end if
jpayne@0:             mkdir ./${name}
jpayne@0:         #if $forward.is_of_type("fastq.gz","fastqsanger.gz")
jpayne@0:             && cp $forward ./${name}/${name}_R1.fastq.gz
jpayne@0:         #else if $forward.is_of_type("fastq.bz2", "fastqsanger.bz2")
jpayne@0:             && tar -vxjOf $forward > ./${name}/${name}_R1.fastq
jpayne@0:         #else
jpayne@0:             && cp $forward ./${name}/${name}_R1.fastq
jpayne@0:         #end if
jpayne@0:         #if $reverse.is_of_type("fastq.gz","fastqsanger.gz")
jpayne@0:             && cp $reverse ./${name}/${name}_R2.fastq.gz
jpayne@0:         #else if $reverse.is_of_type("fastq.bz2", "fastqsanger.bz2")
jpayne@0:             && tar -vxjOf $reverse > ./${name}/${name}_R2.fastq
jpayne@0:         #else
jpayne@0:             && cp $reverse ./${name}/${name}_R2.fastq
jpayne@0:         #end if
jpayne@0:         ## !!! confindr in single-threaded mode; race condition bugs in multiple threads !!! ##
jpayne@0:         && confindr.py -i ./${name} -o ./output -t 1
jpayne@0:         && cat ./output/confindr_log.txt
jpayne@0:         && ls -lah ./output/confindr_report.csv
jpayne@0: 
jpayne@0:     ]]></command>
jpayne@0:     <inputs>
jpayne@0:         <conditional name="reads">
jpayne@0:             <param name="reads_select" type="select" label="Paired-end collection, or two datasets from your history">
jpayne@0:                 <option value="collection">Paired collection from your history</option>
jpayne@0:                 <option value="history">Two FASTQ datasets from your history</option>
jpayne@0:             </param>
jpayne@0:             <when value="collection">
jpayne@0:                 <param label="Paired reads" name="coll" type="data_collection" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" collection_type="paired" />
jpayne@0:             </when>
jpayne@0:             <when value="history">
jpayne@0:                 <param label="Forward reads" type="data" name="forward" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" />
jpayne@0:                 <param label="Reverse reads" type="data" name="reverse" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" />
jpayne@0:             </when>
jpayne@0:         </conditional>
jpayne@0:     </inputs>
jpayne@0:     <outputs>
jpayne@0:         <data format="csv" name="contam_report" label="Contamination Report" from_work_dir="./output/confindr_report.csv" />
jpayne@0:     </outputs>
jpayne@0:     <tests>
jpayne@0:         <test>
jpayne@0:             <param name="reads_select" value="collection" />
jpayne@0:             <param name="coll">
jpayne@0:                 <collection type="paired">
jpayne@0:                     <element name="forward" value="example_R1.fastq.gz" ftype="fastqsanger.gz" />
jpayne@0:                     <element name="reverse" value="example_R2.fastq.gz" ftype="fastqsanger.gz" />
jpayne@0:                 </collection>
jpayne@0:             </param>
jpayne@0:             <output name="contam_report" value="confindr_report.csv" />
jpayne@0:         </test>
jpayne@0:         <test>
jpayne@0:             <param name="reads_select" value="history" />
jpayne@0:             <param name="forward" value="example_R1.fastq.gz" ftype="fastqsanger.gz"/>
jpayne@0:             <param name="reverse" value="example_R2.fastq.gz" ftype="fastqsanger.gz"/>
jpayne@0:             <output name="contam_report" value="confindr_report_2.csv" />
jpayne@0:         </test>
jpayne@0:         <test>
jpayne@0:             <param name="reads_select" value="history" />
jpayne@0:             <param name="forward" value="example_R1.fastq.bz2" ftype="fastqsanger.bz2"/>
jpayne@0:             <param name="reverse" value="example_R2.fastq.bz2" ftype="fastqsanger.bz2"/>
jpayne@0:             <output name="contam_report" value="confindr_report_2.csv" />
jpayne@0:         </test>
jpayne@0:     </tests>
jpayne@0:     <help><![CDATA[
jpayne@0:         ConFindr, a contamination screen for Illumina sequencing
jpayne@0:     ]]></help>
jpayne@0:     <citations>
jpayne@0:         <citation type="doi">10.7717/peerj.6995</citation>
jpayne@0:         <citation type="bibtex">
jpayne@0: @misc{githubConFindr,
jpayne@0:   author = {LastTODO, FirstTODO},
jpayne@0:   year = {TODO},
jpayne@0:   title = {ConFindr},
jpayne@0:   publisher = {GitHub},
jpayne@0:   journal = {GitHub repository},
jpayne@0:   url = {https://github.com/OLC-Bioinformatics/ConFindr},
jpayne@0: }</citation>
jpayne@0:     </citations>
jpayne@2: </tool>