<tool id="shigatyper" name="ShigaTyper" version="1.0.5">
    <description>Shigella genoserotyping</description>
    <requirements>
        <requirement type="package" version="1.0.5">shigatyper</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        #if $reads.reads_select == 'collection'
            #set forward=$reads.coll.forward
            #set reverse=$reads.coll.reverse
            #set name=$reads.coll.name
        #else
            #set name=$reads.coll.forward.name.split('_')[0]
        #end if

        shigatyper -n "$name" "$forward" "$reverse" -vv >

        #if $reads.reads_select == 'collection'
            ${serotype_from_collection}
        #else
            ${serotype_from_history}
        #end if
    ]]></command>
    <inputs>
        <conditional name="reads">
            <param name="reads_select" type="select" label="Paired-end collection, or two datasets from your history">
                <option value="collection">Paired collection from your history</option>
                <option value="history">Two FASTQ datasets from your history</option>
            </param>
            <when value="collection">
                <param label="Paired reads" name="coll" type="data_collection" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" collection_type="paired" />
            </when>
            <when value="history">
                <param label="Forward reads" type="data" name="forward" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" />
                <param label="Reverse reads" type="data" name="reverse" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" />
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data label="${reads.coll.name} Shigella serotype determination" name="serotype_from_collection" format="sam">
            <filter>reads['reads_select'] == 'collection'</filter>
        </data>
        <data label="${reads.forward.name.split('_')[0]} Shigella serotype determination" name="serotype_from_history" format="sam">
            <filter>reads['reads_select'] == 'history'</filter>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="reads_select" value="history" />
            <param name="forward" value="CFSAN029786_S10_L001_R1_001.fastq.gz"/>
            <param name="reverse" value="CFSAN029786_S10_L001_R2_001.fastq.gz"/>
            <output name="serotype_from_history" file="output.tabular"/>
        </test>
        <test>
            <param name="reads_select" value="collection" />
            <param name="coll">
                <collection type="paired">
                    <element name="forward" value="CFSAN029786_S10_L001_R1_001.fastq.gz" ftype="fastqsanger.gz" />
                    <element name="reverse" value="CFSAN029786_S10_L001_R2_001.fastq.gz" ftype="fastqsanger.gz" />
                </collection>
            </param>
            <output name="serotype_from_collection" value="output.tabular" />
        </test>
    </tests>
    <help><![CDATA[
usage: shigatyper [-h] [-n SAMPLE_NAME] [--verbose] [--version] read1 read2

positional arguments:
  read1
  read2


    ]]></help>
    <citations>
        <citation type="bibtex">
@misc{githubshigatyper,
  author = Wu Y1, Lau HK, Lee T, Lau DK, Payne J.
  year = 2019,
  title = In Silico Serotyping Based on Whole-Genome Sequencing Improves the Accuracy of Shigella Identification,
  publisher = AEM,
  journal = Appl Environ Microbiol. ,
  url = https://www.ncbi.nlm.nih.gov/pubmed/30709819,
}</citation>
    </citations>
</tool>