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9
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1 <tool id="bed_clean" name="bed_clean">
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2 <description>clean up BED files</description>
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3 <command interpreter="python">bed_clean.py $input $genome $output > $log </command>
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4 <inputs>
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5 <param name="input" type="data" format="interval" label="Original interval file"/>
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6
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7 <param name="genome" type="select" label="Select chromsome size file" >
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8 <options from_file="chrsize.loc">
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9 <column name="name" index="0"/>
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10 <column name="value" index="1"/>
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11 </options>
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12 </param>
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13
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14 </inputs>
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15 <outputs>
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16 <data format="input" name="output" label="${tool.name} on ${on_string} (interval)"/>
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17 <data format="txt" name="log" label="${tool.name} on ${on_string} (log)"/>
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18 </outputs>
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19 <help>
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20
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21 **Description**
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22
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23 remove lines that are
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24
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25 1. comment or track name lines
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26
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27 2. on chr*_random
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28
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29 3. or have negative coordinates
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30
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31 4. or the end is larger than chromosome size
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32
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33 5. convert strand * to +
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34
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35
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36 </help>
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37 </tool>
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