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1 <tool id="CountReadGCPercent" name="count read GC percent">
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2 <description>Count GC percent for each read against a genome.</description>
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3 <requirements>
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4 <requirement type="set_environment">PYTHONPATH</requirement>
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5 </requirements>
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6 <command interpreter="python"> ../Java/Python/CountReadGCPercent.py -i $inputFastaFile -j $inputGffFile -o $outputFile</command>
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7 <inputs>
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8 <param name="inputFastaFile" type="data" label="Input reference fasta File" format="fasta"/>
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9 <param name="inputGffFile" type="data" label="Input File" format="gff3"/>
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10 </inputs>
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11
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12 <outputs>
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13 <data format="gff3" name="outputFile" label="[count read GC percent] Output File"/>
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14 </outputs>
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15
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16 <help>
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17 Count the GC% of a FASTA file.
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18 </help>
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19 </tool>
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