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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> |
