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1 <tool id="bedclean" name="clean interval">
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2 <description>remove off-chromosome lines</description>
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3 <command interpreter="python">bedclean.py $input $genome $output > $log </command>
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4 <inputs>
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5 <param name="input" type="data" format="interval" label="Original interval file"/>
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6 <param name="genome" type="select" label="Select genome">
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7 <option value="/Users/xuebing/galaxy-dist/tool-data/genome/chrsize/mouse.mm9.genome" selected="true">mm9</option>
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8 <option value="/Users/xuebing/galaxy-dist/tool-data/genome/chrsize/mouse.mm8.genome">mm8</option>
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9 <option value="/Users/xuebing/galaxy-dist/tool-data/genome/chrsize/human.hg18.genome">hg18</option>
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10 <option value="/Users/xuebing/galaxy-dist/tool-data/genome/chrsize/human.hg19.genome">hg19</option>
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11 </param>
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12 </inputs>
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13 <outputs>
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14 <data format="input" name="output" label="${tool.name} on ${on_string} (interval)"/>
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15 <data format="txt" name="log" label="${tool.name} on ${on_string} (log)"/>
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16 </outputs>
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17 <help>
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18
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19 **Description**
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20
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21 remove lines that are
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22
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23 1. comment or track name lines
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24
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25 2. on chr*_random
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26
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27 3. or have negative coordinates
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28
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29 4. or the end is larger than chromosome size
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30
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31
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32 </help>
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33 </tool>
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