Mercurial > repos > xuebing > sharplabtool
comparison tools/encode/random_intervals.xml @ 0:9071e359b9a3
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| author | xuebing |
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| date | Fri, 09 Mar 2012 19:37:19 -0500 |
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| -1:000000000000 | 0:9071e359b9a3 |
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| 1 <tool id="random_intervals1" name="Random Intervals"> | |
| 2 <description>create a random set of intervals</description> | |
| 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> | |
| 4 <inputs> | |
| 5 <param name="input1" type="data" format="interval" label="File to Mimick"> | |
| 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."/> | |
| 7 </param> | |
| 8 <param name="input2" type="data" format="interval" label="Intervals to Mask"/> | |
| 9 <param name="use_mask" type="select" label="Use mask"> | |
| 10 <option value="no_mask">No</option> | |
| 11 <option value="use_mask">Yes</option> | |
| 12 </param> | |
| 13 <param name="strand_overlaps" type="select" label="Allow overlaps"> | |
| 14 <option value="all">Any</option> | |
| 15 <option value="strand">Across Strands</option> | |
| 16 <option value="none">None</option> | |
| 17 </param> | |
| 18 <param name="regions" type="select" label="Regions to use"> | |
| 19 <options from_file="regions.loc"> | |
| 20 <column name="name" index="2"/> | |
| 21 <column name="value" index="1"/> | |
| 22 <column name="dbkey" index="0"/> | |
| 23 <filter type="data_meta" ref="input1" key="dbkey" column="0" /> | |
| 24 <validator type="no_options" message="This tool currently only works with ENCODE data from genome builds hg16 or hg17."/> | |
| 25 </options> | |
| 26 </param> | |
| 27 </inputs> | |
| 28 <outputs> | |
| 29 <data name="out_file1" format="input"/> | |
| 30 </outputs> | |
| 31 <help> | |
| 32 | |
| 33 .. class:: warningmark | |
| 34 | |
| 35 This tool currently only works with ENCODE data from genome builds hg16 or hg17. | |
| 36 | |
| 37 ----- | |
| 38 | |
| 39 .. class:: infomark | |
| 40 | |
| 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. | |
| 42 | |
| 43 ----- | |
| 44 | |
| 45 **Syntax** | |
| 46 | |
| 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. | |
| 48 | |
| 49 **Allow overlaps** options | |
| 50 * **Across Strands** - random regions are allowed to overlap only if they are on different strands. | |
| 51 * **Any** - all overlaps are allowed. | |
| 52 * **None** - no overlapping regions are allowed. | |
| 53 | |
| 54 **Regions to use** options | |
| 55 * Bounding region of interest based on the dataset build. | |
| 56 | |
| 57 </help> | |
| 58 </tool> |