root/galaxy-central/tools/encode/random_intervals.xml

リビジョン 2, 2.6 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central

行番号 
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
35This 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
47This 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>
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