debaser.xml

<tool id="debaser" name="DeBaser" version="0.1.0">
    <requirements>
        <requirement type="package">bowtie2</requirement>
        <requirement type="package" version="1.2">samtools</requirement>
        <requirement type="package">angsd</requirement>
        <requirement type="package" version="1.2.1">htslib</requirement>
    </requirements>
    <!-- A note on conditionals: their names are used in the code block but not test block -->
    <!-- this means that you can't have the same parameter names in both sides of the conditional -->
    <!-- because this would mess up the testing. As a result the code block ends up with unavoidable -->
    <!-- duplications. -->
    <command detect_errors="exit_code"><![CDATA[
        mkdir variety_dir &&
        #set $input_filename = '.'.join(str($infile.element_identifier).split('.')[:-1]) + '.fasta'
        ln -s '$infile' '${input_filename}' &&
        #if str($read_mode.paired_read_mode) == "paired":
          #if $read_mode.variety_paired.forward.metadata.is_gzipped
            #set $extension = 'fastq.gz'
          #else
            #set $extension = 'fastq'
          #end if
          ln -s '$read_mode.variety_paired.forward' 'variety_dir/${read_mode.variety_paired.name}_1.$extension' &&
          ln -s '$read_mode.variety_paired.reverse' 'variety_dir/${read_mode.variety_paired.name}_2.$extension' &&
        #else
          #if $read_mode.variety_single.metadata.is_gzipped
            #set $extension = 'fastq.gz'
          #else
            #set $extension = 'fastq'
          #end if
          #set $read_filename = '.'.join(str($read_mode.variety_single.name).split('.')[:-1])
          ln -s '$read_mode.variety_single' 'variety_dir/${read_filename}_1.$extension' &&
          #end if
        python $__tool_directory__/debaser.py
        --infile './$input_filename'
        --reference '$reference'
        --variety variety_dir
        --output output &&
        mv output/*.fa $output1
    ]]></command>
    <inputs>
        <param type="data" format="fasta" name="infile" label="input file"></param>
        <param type="data" format="fasta" name="reference" label="reference genome"></param>
        <conditional name="read_mode">
          <param name="paired_read_mode" checked="True" truevalue="paired" falsevalue="single" type="boolean" label="Reads are in read pairs" />
          <when value="paired">
            <param type="data_collection" collection_type="paired" format="fastqsanger,fastqsanger.gz" name="variety_paired"></param>
          </when>
          <when value="single">
            <param type="data" format="fastqsanger,fastqsanger.gz" name="variety_single"></param>
          </when>
        </conditional>
    </inputs>
    <outputs>
        <data name="output1" format="fasta" />
            <!-- <collection name="consensus" type="list" label="consensus of varieties from ${on_string}"> -->
                <!-- <discover_datasets pattern="(?P&lt;name&gt;.*)\.fa" ext="fasta" directory="output"/> -->
            <!-- </collection> -->
    </outputs>
    <tests>
        <test>
            <param name="infile" value="small.fasta"/>
            <param name="reference" value="Mesculenta_305_v6.1.cds.fa"/>
            <param name="paired_read_mode" value="paired" />
            <param name="variety_paired">
              <collection type="paired" name="small">
                <element name="forward" value="small_reads_1.fastq"/>
                <element name="reverse" value="small_reads_2.fastq"/>
              </collection>
            </param>
            <output name="output1" value="small_paired_output.fasta" ftype="fasta" />
        </test>
        <test>
            <param name="infile" value="small.fasta"/>
            <param name="reference" value="Mesculenta_305_v6.1.cds.fa"/>
            <param name="paired_read_mode" value="single" />
            <param name="variety_single" value="small_reads_1.fastq" />
            <output name="output1" value="small_single_output.fasta" ftype="fasta" />
        </test>
    </tests>

    <help><![CDATA[
        Find polymorphisms in plant varieties
    ]]></help>
    <citations>
        <citation type="bibtex">
            @misc{debaser,
            author = {Juma, John; Eyles, Rodney; Shah, Trushar },
            year = {2017},
            title = {DeBaser: An integrated tool for fast NGS data assembly, multi-sequence alignment and sequence variation detection in plants},
            publisher = {GitHub},
            journal = {GitHub Repository},
            url = {https://github.com/ajodeh-juma/debaser-galaxy/},
            }
        </citation>
    </citations>
</tool>