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1 <tool id="readPerContig" name="readPerContig" version="1.0">
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2 <description>
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3 This script counts the number of read per contig using a Blat output.
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4 Output is a 2 column tabular file.
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5 </description>
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6 <command interpreter="perl">readPerContig.pl-r $reference -id $identity -cov $coverage -b blat_result -v 0 -s $statistics -o $output</command>
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7 <inputs>
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8 <param name="reference" type="data" format="fasta" label="References."/>
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9 <param name="blat" type="data" format="psl" label="Blat .psl output file."/>
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10 <param name="identity" type="integer" value="95" label="Identity threshold."/>
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11 <param name="coverage" type="integer" value="60" label="Coverage threshold."/>
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12 <param name="statistics" type="select" label="Statistics to print">
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13 <option value="nb_reads">Read number</option>
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14 <option value="rpkm">RPKM</option>
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15 <option value="mean_coverage">Mean coverage</option>
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16 </param>
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17 </inputs>
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18 <outputs>
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19 <data name="output" format="tabular"/>
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20 </outputs>
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21 </tool>
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