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1 <tool id="RNASeQC" name="RNASeQC">
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2 <description>RNASeQC: Quality control metrics for RNA-seq data</description>
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3 <requirements>
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4
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4 <requirement type="package" version="1.2.8">zlib</requirement>
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5 <requirement type="package" version="0.6.2">bwa</requirement>
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3
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6 <requirement type="set_environment">RNASEQCPATH</requirement>
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7 </requirements>
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8 <command interpreter="java">
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9 -jar \$RNASEQCPATH/RNASeQC.jar -r $input1 -t $input2 -s "SampleID|$input3|Notes" -o output
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10 </command>
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11
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12 <inputs>
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13
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14 <param name="input1" type="data" format="fasta" label="Reference genome"/>
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15 <param name="input2" type="data" format="gtf" label="File Defining transcipts"/>
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16 <param name="input4" type="data" format="bam" label="BAM File"/>
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17
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18 </inputs>
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19
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20 <outputs>
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21 <data format="txt" name="output" label="output file" />
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22 </outputs>
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23
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24 <help>
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25 This tool computes GC content from a FASTA file.
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26 </help>
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27
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28 </tool>
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