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1 <?xml version="1.0"?>
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2 <tool id="cutClust_1" name="cutClust">
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3 <description>Remove clusters below a certain depth</description>
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4 <command >cut -f $depth- $inputFile | sed '/^$/d' | sort | uniq > $outputfile</command>
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5 <inputs>
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6 <param format="tabular" name="inputFile" type="data" label="Columnar Input File" help="tabular file of DNAclust clusters" />
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7 <param name="depth" size="10" type="text" value="50" label="Minimum depth for cutoff" />
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8
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9 </inputs>
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10 <outputs>
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11 <data format="tabular" name="outputfile" />
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12 </outputs>
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13 <help>
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14 .. class:: infomark
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15
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16 **TIP**
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17
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18 ::
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19
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20 This tool simply cuts off columns from the left
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21 e.g. set to 2 to remove singletons, 50 to remove clusters with less than 50 reads
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22 </help>
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23
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24
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25 </tool>
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