jpayne@0: <tool id="shigatyper" name="ShigaTyper" version="1.0.5">
jpayne@0:     <description>Shigella genoserotyping</description>
jpayne@0:     <requirements>
jpayne@0:         <requirement type="package" version="1.0.5">shigatyper</requirement>
jpayne@0:     </requirements>
jpayne@0:     <command detect_errors="exit_code"><![CDATA[
jpayne@2:         #if $reads.reads_select == 'collection'
jpayne@2:             #set forward=$reads.coll.forward
jpayne@2:             #set reverse=$reads.coll.reverse
jpayne@2:             #set name=$reads.coll.name
jpayne@2:         #else
jpayne@2:             #set name=$reads.coll.forward.name.split('_')[0]
jpayne@2:         #end if
jpayne@2: 
jpayne@2:         shigatyper -n "$name" "$forward" "$reverse" -vv >
jpayne@2: 
jpayne@2:         #if $reads.reads_select == 'collection'
jpayne@2:             ${serotype_from_collection}
jpayne@2:         #else
jpayne@2:             ${serotype_from_history}
jpayne@2:         #end if
jpayne@0:     ]]></command>
jpayne@0:     <inputs>
jpayne@2:         <conditional name="reads">
jpayne@2:             <param name="reads_select" type="select" label="Paired-end collection, or two datasets from your history">
jpayne@2:                 <option value="collection">Paired collection from your history</option>
jpayne@2:                 <option value="history">Two FASTQ datasets from your history</option>
jpayne@2:             </param>
jpayne@2:             <when value="collection">
jpayne@2:                 <param label="Paired reads" name="coll" type="data_collection" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" collection_type="paired" />
jpayne@2:             </when>
jpayne@2:             <when value="history">
jpayne@2:                 <param label="Forward reads" type="data" name="forward" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" />
jpayne@2:                 <param label="Reverse reads" type="data" name="reverse" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" />
jpayne@2:             </when>
jpayne@2:         </conditional>
jpayne@0:     </inputs>
jpayne@0:     <outputs>
jpayne@2:         <data label="${reads.coll.name} Shigella serotype determination" name="serotype_from_collection" format="sam">
jpayne@2:             <filter>reads['reads_select'] == 'collection'</filter>
jpayne@2:         </data>
jpayne@2:         <data label="${reads.forward.name.split('_')[0]} Shigella serotype determination" name="serotype_from_history" format="sam">
jpayne@2:             <filter>reads['reads_select'] == 'history'</filter>
jpayne@2:         </data>
jpayne@0:     </outputs>
jpayne@0:     <tests>
jpayne@0:         <test>
jpayne@2:             <param name="reads_select" value="history" />
jpayne@2:             <param name="forward" value="CFSAN029786_S10_L001_R1_001.fastq.gz"/>
jpayne@2:             <param name="reverse" value="CFSAN029786_S10_L001_R2_001.fastq.gz"/>
jpayne@2:             <output name="serotype_from_history" file="output.tabular"/>
jpayne@2:         </test>
jpayne@2:         <test>
jpayne@2:             <param name="reads_select" value="collection" />
jpayne@2:             <param name="coll">
jpayne@2:                 <collection type="paired">
jpayne@2:                     <element name="forward" value="CFSAN029786_S10_L001_R1_001.fastq.gz" ftype="fastqsanger.gz" />
jpayne@2:                     <element name="reverse" value="CFSAN029786_S10_L001_R2_001.fastq.gz" ftype="fastqsanger.gz" />
jpayne@2:                 </collection>
jpayne@2:             </param>
jpayne@2:             <output name="serotype_from_collection" value="output.tabular" />
jpayne@0:         </test>
jpayne@0:     </tests>
jpayne@0:     <help><![CDATA[
jpayne@0: usage: shigatyper [-h] [-n SAMPLE_NAME] [--verbose] [--version] read1 read2
jpayne@0: 
jpayne@0: positional arguments:
jpayne@0:   read1
jpayne@0:   read2
jpayne@0: 
jpayne@0: 
jpayne@0:     ]]></help>
jpayne@0:     <citations>
jpayne@0:         <citation type="bibtex">
jpayne@0: @misc{githubshigatyper,
jpayne@2:   author = Wu Y1, Lau HK, Lee T, Lau DK, Payne J.
jpayne@2:   year = 2019,
jpayne@2:   title = In Silico Serotyping Based on Whole-Genome Sequencing Improves the Accuracy of Shigella Identification,
jpayne@2:   publisher = AEM,
jpayne@2:   journal = Appl Environ Microbiol. ,
jpayne@2:   url = https://www.ncbi.nlm.nih.gov/pubmed/30709819,
jpayne@0: }</citation>
jpayne@0:     </citations>
jpayne@0: </tool>