view chimerascan.xml @ 2:ec38f053b647 draft

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<tool id="chimerascan" name="ChimeraScan">
    <description>A tool for identifying chimeric transcription in sequencing data.</description>
    <command detect_errors="exit_code">
            bash $__tool_directory__/run.sh && python $__tool_directory__/chimerascan_run.py -p 8 $__tool_directory__/myindex 
            #if $input_type_conditional.chimerascan_input_type == "paired"
                    $input_type_conditional.input_1 $input_type_conditional.input_2
            #else
                    $input_type_conditional.input.forward $input_type_conditional.input.reverse
            #end if
            $galaxy_output
    </command>
    <inputs>
        <conditional name="input_type_conditional">
            <param name="chimerascan_input_type" type="select" label="Input Type" help="Select between paired and paired collection">
                    <option value="paired" selected="true">Paired</option>
                    <option value="paired_collection">Paired Collection</option>
            </param>
            <when value="paired">
                    <param format='fastq' name='input_1' type='data' label='FASTQ file, forward reads' />
                    <param format='fastq' name='input_2' type='data' label='FASTQ file, reverse reads' />
            </when>
            <when value="paired_collection">
                    <param format="fastq" name='input' type="data_collection" collection_type="paired" label="Select a paired collection" help="Specify paired dataset collection containing paired reads"/>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data name="galaxy_output" format="bed" />
    </outputs>

    <tests>
        <test>
            <param name="input1" value="input1.fastq"/>
            <param name="input2" value="input2.fastq"/>
            <output name="galaxy_output" file="outputfile.bed" ftype="bed"/>
        </test>
        <test>
            <param name="fastq_input">
              <collection type="paired">
                <element name="forward" value="input1.fastq" />
                <element name="reverse" value="input2.fastq" />
              </collection>
            </param>
            <param name="input_type" value="paired_collection" />
            <output name="galaxy_output" file="outputfile.bed" ftype="bed"/>
        </test>
    </tests>

    <help>
	Bowtie index files must be placed inside 'myindex folder'
        A tool for identifying chimeric transcription in sequencing data.
    </help>

</tool>