Mercurial > repos > yqiancolumbia > ctk_test
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author | yqiancolumbia |
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date | Mon, 30 Apr 2018 05:25:11 -0400 |
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1 <tool id="tag2cluster" name="Cluster genomic regions"> |
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2 <command interpreter="perl"> |
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3 /home/galaxy/tools/CTK/tag2cluster.pl -v $bigFile $strand -maxGap $MaxGap $input $output |
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4 </command> |
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5 <inputs> |
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6 <param type="data" format="bed" name="input" label="Input BED file of unique CLIP tags (.gz file accepted)"/> |
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7 |
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8 <param name="bigFile" type="boolean" truevalue="-big" falsevalue="" checked="no" label="This is a big file (over 6M lines)" /> |
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9 <param name="strand" type="boolean" truevalue="-s" falsevalue="" checked="yes" label="Same strand required" /> |
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10 <param name="MaxGap" type="integer" value="-1" label="The max gap to be considered as an overlap" /> |
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11 |
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12 </inputs> |
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13 <outputs> |
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14 <data name="output" format="bed" /> |
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15 </outputs> |
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16 <help> |
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17 .. class:: infomark |
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18 |
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19 **What it does** |
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20 |
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21 This tool will cluster overlapping tags or nearby regions into clusters and report tag count in each cluster. |
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22 It will take as input files in BED format of unique CLIP tags and output files in BED format of clustered overlapping CLIP tags. |
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23 |
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24 </help> |
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25 |
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26 </tool> |