[2] | 1 | <tool id="random_intervals1" name="Random Intervals">
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| 2 | <description>create a random set of intervals</description>
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| 3 | <command interpreter="python">random_intervals_no_bits.py $regions $input2 $input1 $out_file1 ${input2.metadata.chromCol} ${input2.metadata.startCol} ${input2.metadata.endCol} ${input1.metadata.chromCol} ${input1.metadata.startCol} ${input1.metadata.endCol} ${input1.metadata.strandCol} $use_mask $strand_overlaps ${GALAXY_DATA_INDEX_DIR}</command>
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| 4 | <inputs>
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| 5 | <param name="input1" type="data" format="interval" label="File to Mimick">
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| 6 | <validator type="unspecified_build" message="Unspecified build, this tool works with data from genome builds hg16 or hg17. Click the pencil icon in your history item to set the genome build."/>
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| 7 | </param>
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| 8 | <param name="input2" type="data" format="interval" label="Intervals to Mask"/>
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| 9 | <param name="use_mask" type="select" label="Use mask">
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| 10 | <option value="no_mask">No</option>
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| 11 | <option value="use_mask">Yes</option>
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| 12 | </param>
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| 13 | <param name="strand_overlaps" type="select" label="Allow overlaps">
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| 14 | <option value="all">Any</option>
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| 15 | <option value="strand">Across Strands</option>
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| 16 | <option value="none">None</option>
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| 17 | </param>
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| 18 | <param name="regions" type="select" label="Regions to use">
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| 19 | <options from_file="regions.loc">
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| 20 | <column name="name" index="2"/>
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| 21 | <column name="value" index="1"/>
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| 22 | <column name="dbkey" index="0"/>
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| 23 | <filter type="data_meta" ref="input1" key="dbkey" column="0" />
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| 24 | <validator type="no_options" message="This tool currently only works with ENCODE data from genome builds hg16 or hg17."/>
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| 25 | </options>
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| 26 | </param>
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| 27 | </inputs>
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| 28 | <outputs>
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| 29 | <data name="out_file1" format="input"/>
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| 30 | </outputs>
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| 31 | <help>
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| 32 |
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| 33 | .. class:: warningmark
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| 34 |
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| 35 | This tool currently only works with ENCODE data from genome builds hg16 or hg17.
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| 36 |
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| 37 | -----
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| 38 |
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| 39 | .. class:: infomark
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| 40 |
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| 41 | **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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| 42 |
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| 43 | -----
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| 44 |
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| 45 | **Syntax**
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| 46 |
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| 47 | 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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| 48 |
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| 49 | **Allow overlaps** options
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| 50 | * **Across Strands** - random regions are allowed to overlap only if they are on different strands.
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| 51 | * **Any** - all overlaps are allowed.
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| 52 | * **None** - no overlapping regions are allowed.
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| 53 |
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| 54 | **Regions to use** options
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| 55 | * Bounding region of interest based on the dataset build.
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| 56 |
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| 57 | </help>
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| 58 | </tool> |
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