view RNASeQC.xml @ 8:aad08b24baff default tip

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<tool id="RNASeQC" name="RNASeQC">
	<description>RNASeQC: Quality control metrics for RNA-seq data</description>
	<requirements>
		<requirement type="package" version="1.2.8">zlib</requirement>
		<requirement type="package" version="0.6.2">bwa</requirement>
		<requirement type="set_environment">RNASEQCPATH</requirement>
	</requirements>
	<command interpreter="java">
-jar \$RNASEQCPATH/RNASeQC.jar -r $input1 -t $input2 -s "SampleID|$input3|Notes" -o output
	</command>

	<inputs>

	  	<param name="input1" type="data" format="fasta" label="Reference genome"/>
		<param name="input2" type="data" format="gtf" label="File Defining transcipts"/>
		<param name="input4" type="data" format="bam" label="BAM File"/>

	</inputs>

	<outputs>
		<data format="txt" name="output" label="output file" />
    	</outputs>

  <help>
This tool computes GC content from a FASTA file.
  </help>

</tool>