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44 lines
1.9 KiB
XML
44 lines
1.9 KiB
XML
<tool id="random_intervals1" name="Random Intervals">
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<description>create a random set of intervals</description>
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<command interpreter="python2.4">random_intervals_no_bits.py $regions $input2 $input1 $out_file1 $input2_chromCol $input2_startCol $input2_endCol $input1_chromCol $input1_startCol $input1_endCol $input1_strandCol $use_mask $strand_overlaps</command>
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<inputs>
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<page>
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<param name="input1" type="data" format="interval" label="File to Mimick"/>
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<param name="input2" type="data" format="interval" label="Intervals to Mask"/>
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<param name="use_mask" type="select">
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<label>Use Mask</label>
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<option value="no_mask">No</option>
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<option value="use_mask">Yes</option>
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</param>
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<param name="strand_overlaps" type="select">
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<label>Allow overlaps</label>
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<option value="all">Any</option>
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<option value="strand">Across Strands</option>
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<option value="none">None</option>
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</param>
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</page>
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<page>
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<param name="regions" label="Regions to use" type="select" dynamic_options="get_available_data( input1.dbkey )"/>
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</page>
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</inputs>
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<outputs>
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<data name="out_file1" format="bed"/>
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</outputs>
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<help>
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This tool will attempt to create a random set of intervals that mimic those found within your source file. You may also specify a set of intervals to mask.
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There are several overlap options:
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* Across Strands: Random regions are allowed to overlap only if they are on different strands.
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* Any: All overlaps are allowed.
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* None: No overlapping regions are allowed.
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The second step will let you select a bounding region of interest.
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.. class:: infomark
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**Note:** If you do not wish to mask a set of intervals, change the Use Mask option to No, this option will override any Mask files selected.
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</help>
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<code file="random_intervals_code.py"/>
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</tool> |