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<tool id="ctat_star_fusion" name="ctat_star_fusion" version="1.0.1" profile="17.05">

    <description>Fusion-finding Pipeline Using the STAR Aligner</description>
    <requirements>
	<requirement type="package" version="1.4.0">star-fusion</requirement>
    </requirements>
    <!-- Using command's detect_errors instead of below.
    <stdio>
      <exit_code range="1:"  level="fatal"   description="Error returned from pipeline" />
    </stdio>
    <regex match="Must investigate error above."
           source="stderr"
           level="fatal"
           description="Unknown error encountered" />
    -->
    <command detect_errors="default">
      <![CDATA[
      STAR-Fusion
        --genome_lib_dir "${genome_resource_lib.fields.path}"
        --left_fq  "${left_input}"
        --right_fq "${right_input}"
        --output_dir subdir
        --STAR_SortedByCoordinate
      ]]>
    </command>

    <inputs>
      <param format="fastq" name="left_input" type="data" label="Left/Forward strand reads" help=""/>
      <param format="fastq" name="right_input" type="data" label="Right/Reverse strand reads" help=""/>
      <param name="genome_resource_lib" type="select" label="Select a reference genome">
        <options from_data_table="ctat_genome_resource_libs">
          <filter type="sort_by" column="2" />
          <validator type="no_options" message="No indexes are available" />
        </options>
      </param>
    </inputs>

    <outputs>
      <data format="txt" name="starfusion_log" label="${tool.name} on ${on_string}: log" from_work_dir="subdir/Log.out"/>
      <data format="bam" name="aligned_bam" label="${tool.name} on ${on_string}: Aligned Bam" from_work_dir="subdir/std.STAR.bam"/>
      <data format="tabular" name="candidates" label="${tool.name} on ${on_string}: Fusion candidates" from_work_dir="subdir/star-fusion.fusion_predictions.abridged.tsv"/>
      <data format="tabular" name="chimeric_junc" label="${tool.name} on ${on_string}: Chimeric.out.junction" from_work_dir="subdir/std.Chimeric.out.junction"/> 
    </outputs>
    <tests>
      <test>
        <param name="left_input" value="StarFusion/reads_1.fq.gz" />
        <param name="right_input" value="StarFusion/reads_2.fq.gz" />
        <!--
        <param name="left_input" value="reads.left.simPE.fq" />
        <param name="right_input" value="reads.right.simPE.fq" />
        -->
        <!-- FIX - now that we added the CTAT ref lib path as a parameter, how do we find it for testing?
        <param name="genome_resource_lib.fields.path" value="?????" />
        -->
        <!--
        <output name="aligned_bam" file="SF_out_aligned.bam" />
        <output name="candidates" file="SF_out_fusion_candidates.dat" />
        <output name="chimeric_junc" file="SF_out_chimeric.junction" />
        <output name="starfusion_log" file="SF_out.log" />
        -->
        <output name="starfusion_log">
            <assert_contents>
               <has_line_matching expression=".+" />
               <has_line line="ALL DONE!" />
            </assert_contents>
        </output>
        <output name="aligned_bam">
            <assert_contents>
               <has_line_matching expression=".+" />
               <!-- The following checks for the magic number at the start of the bam file -->
               <!-- At first I thought "\x8B\x1F" was the number, but it turns out the file
                    produced by the StarFusion test had that sequence in the file somewhere else.
               -->
               <has_text_matching expression="\x1F\x8B" />
            </assert_contents>
        </output>
        <output name="candidates">
            <assert_contents>
               <has_line_matching expression=".+" />
               <has_line line="#fusion_name&#009;JunctionReads&#009;SpanningFrags&#009;Splice_type&#009;LeftGene&#009;LeftBreakpoint&#009;RightGene&#009;RightBreakpoint&#009;Long_double_anchor_support" />
            </assert_contents>
        </output>
        <output name="chimeric_junc">
            <assert_contents>
               <has_line_matching expression=".+" />
               <has_line_matching expression="^chr20.*" />
            </assert_contents>
        </output>
      </test>
    </tests>
    <help>
.. class:: infomark

STAR-Fusion is a component of the Trinity Cancer Transcriptome Analysis Toolkit (CTAT). STAR-Fusion uses the STAR aligner to identify candidate fusion transcripts supported by Illumina reads. STAR-Fusion further processes the output generated by the STAR aligner to map junction reads and spanning reads to a reference annotation set. Please read more here_.

.. _here: https://github.com/STAR-Fusion/STAR-Fusion/wiki

    </help>
</tool>