annotate trinityctatfusion/star_fusion_new.xml @ 0:887986b43271 draft default tip

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<tool id="star-fusion-new" name="Star-fusion-new" version="0.0.2">
    <description>Fusion-finding Pipeline using the STAR aligner</description>
    <command>
    sh star_fusion_toolshed_wrapper.sh
    $left_input
    $right_input
    "subdir" 
    </command>
    <macros>
    </macros>
    <stdio>
      <exit_code range="1:"  level="fatal"   description="Error returned from pipeline" />
    </stdio>
    <regex match="Must investigate error above."
           source="stderr"
           level="fatal"
           description="Unknown error encountered" />
    <inputs>
      <param format="fastq" name="left_input" type="data" label="Left/Forward strand reads" help=""/>
      <param format="fastq" name="right_input" type="data" label="Right/Reverse strand reads" help=""/>
    </inputs>
    <outputs>
      <data format="txt" name="starfusion_log" label="${tool.name} on ${on_string}: log" from_work_dir="subdir/Log.out"/>
      <data format="bam" name="aligned_bam" label="${tool.name} on ${on_string}: Aligned Bam" from_work_dir="subdir/Aligned.sortedByCoord.out.bam"/>
      <data format="tabular" name="candidates" label="${tool.name} on ${on_string}: Fusion candidates" from_work_dir="subdir/star-fusion.fusion_candidates.final.abridged"/>
      <data format="tabular" name="chimeric_junc" label="${tool.name} on ${on_string}: Chimeric.out.junction" from_work_dir="subdir/Chimeric.out.junction"/> 
    </outputs>
    <tests>
      <test>
        <param name="left_input" value="left.fq" />
	<param name="right_input" value="right.fq" />
        <output name="aligned_bam" file="Aligned.out.bam"/>
	<output name="chimeric_junction" file="chimeric.out.junction"/>
      </test>
    </tests>
    <help>
        STAR-fusion New
    </help>
</tool>