<tool id="discasm" name="DISCASM" version="1.0.0" profile="17.05">
    <description>Discordant and Unmapped Read De novo Transcriptome Assembly</description>
    <requirements>
        <!-- Added following requirement, but it does not exist in conda yet. -->
        <requirement type="package" version="0.1.2">discasm</requirement>
    </requirements>
    <!--
        <requirement type="set_environment">TRINTOOLS</requirement> 
        echo $TRINTOOLS
            /N/dc2/projects/galaxyshared/trinity/third_party_applications
        But this is only on github. Looks like we need to create a conda package for this one.
    -->
    <command detect_errors="default">
      DISCASM
      --aligned_bam $bam 
      --chimeric_junctions $chimeric 
      --left_fq $left_input
      --right_fq $right_input
      --denovo_assembler OasesMultiK 
      --out_dir "subdir"
    </command>
    <stdio>
      <exit_code range="1:"  level="fatal"   description="Error returned from pipeline" />
    </stdio>
    <regex match="Must investigate error above."
           source="stderr"
           level="fatal"
           description="Unknown error encountered" />
    <inputs>
      <param format="bam" name="bam" type="data" label="Aligned bam" help="Aligned Bam from Star Fusion tool"/>
      <param format="tabular" name="chimeric" type="data" label="Chimeric.out.junction" help="Chimeric junction from Star Fusion tool"/>
      <param format="fastq" name="left_input" type="data" label="Left/Forward strand reads" help="Forward strand reads"/>
      <param format="fastq" name="right_input" type="data" label="Right/Reverse strand reads" help="Reverse strand reads"/>
    </inputs>
    <outputs>
      <data format="fasta" name="oases.transcripts" label="${tool.name} on ${on_string}: Oasis Transcripts" from_work_dir="subdir/oasesMultiK_out_dir/oases.transcripts.fa" />
    </outputs>

    <tests>
      <test>
        <!-- The aligned and chimeric I got off of the website don't work with these reads_[1|2].fq.gz inputs.
             These aligned and chimeric were created when I ran the StarFusion test on these inputs.
        -->
        <param name="left_input" value="DISCASM/SF2/reads_1.fq.gz" />
        <param name="right_input" value="DISCASM/SF2/reads_2.fq.gz" />
        <param name="bam" value="DISCASM/SF2/Aligned.sortedByCoord.out.bam" />
        <param name="chimeric" value="DISCASM/SF2/Chimeric.out.junction" />
        <output name="oases.transcripts" file="DISCASM/reads_1_2.oases.transcripts.fa" />
      </test> 
      <test>
        <!-- The Aligned and Chimeric came from a StarFusion test on the reads.[left|right].simPE.fq inputs.
	-->
        <param name="left_input" value="DISCASM/SF1/reads.left.simPE.fq" />
        <param name="right_input" value="DISCASM/SF1/reads.right.simPE.fq" />
        <param name="bam" value="DISCASM/SF1/SF_out_aligned.bam" />
        <param name="chimeric" value="DISCASM/SF1/SF_out_chimeric.junction" />
        <output name="oases.transcripts" file="DISCASM/reads.simPE.oases.transcripts.fa" />
      </test>
    </tests>
    <help>
.. class:: infomark

DISCASM is a component of the Trinity Cancer Transcriptome Analysis Toolkit (CTAT). DISCASM aims to extract reads that map to reference genomes in a discordant fashion and optionally include reads that do not map to the genome at all, and perform a de novo transcriptome assembly of these reads. DISCASM relies on the output from STAR (as run via STAR-Fusion), and supports de novo transcriptome assembly using Trinity or Oases. Please read more here_.

.. _here: https://github.com/DISCASM/DISCASM/wiki
    </help>
    <cite>
    </cite>
</tool>