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1 <tool id="ccat_int2bed" name="CCAT2bed" version="1.0">
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2 <description>Convert CCAT output (intervals) into Bed</description>
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3 <requirements>
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4 <container type="docker">institutcuriengsintegration/ccattobed:1.0</container>
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5 </requirements>
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6 <command interpreter="bash">
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7 ccat2bed.sh -f $inputfile -t $minHeight -o $output -g $genome_selector -n $name -r ${__root_dir__}
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8 </command>
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9 <inputs>
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10 <param name="name" type="text" label="type of experiment" value="track_name"/>
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11 <param name="inputfile" type="data" label="CCAT output interval file" value="CCAT output interval file" format="interval"/>
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12 <param name="genome_selector" type="select" label="Select the genome under study">
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13 <option value="hg19" selected="true">hg19</option>
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14 <option value="hg18">hg18</option>
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15 <option value="mm9">mm9</option>
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16 <option value="mm10">mm10</option>
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17 </param>
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18 <param name="minHeight" type="integer" label="Minimal read count per peak to consider" value="0"/>
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19
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20 </inputs>
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21 <outputs>
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22 <data name="output" format="bed" label="${name}.bed"/>
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23 </outputs>
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24 <help>
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25 **What it does**
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26
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27 This tool creates a .bed file using .peaks output of CCAT
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28
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29 </help>
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30 </tool>
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