root/galaxy-central/tools/new_operations/merge.xml

リビジョン 2, 1.9 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central

行番号 
1<tool id="gops_merge_1" name="Merge">
2  <description>the overlapping intervals of a query</description>
3  <command interpreter="python">gops_merge.py $input1 $output -1 ${input1.metadata.chromCol},${input1.metadata.startCol},${input1.metadata.endCol},${input1.metadata.strandCol} $returntype</command>
4  <inputs>
5    <param format="interval" name="input1" type="data">
6      <label>Merge overlaping regions of</label>
7    </param>
8    <param name="returntype" type="boolean" truevalue="-3" falsevalue="">
9      <label>Output 3 column bed</label>
10    </param>
11   </inputs>
12  <outputs>
13    <data format="input" name="output" metadata_source="input1" />
14  </outputs>
15  <code file="operation_filter.py">
16    <hook exec_after_process="exec_after_merge" />
17  </code>
18  <tests>
19    <test>
20      <param name="input1" value="1.bed" />
21      <output name="output" file="gops-merge.dat" />
22      <param name="returntype" value="true" />
23    </test>
24    <test>
25      <param name="input1" value="2_mod.bed" ftype="interval"/>
26      <output name="output" file="gops_merge_diffCols.dat" />
27      <param name="returntype" value="true" />
28    </test>
29    <test>
30      <param name="input1" value="gops_bigint.interval" />
31      <output name="output" file="gops_merge_out2.bed" />
32      <param name="returntype" value="true" />
33    </test>
34  </tests>
35  <help>
36
37.. class:: infomark
38
39**TIP:** If your query does not appear in the pulldown menu, it means that it is not in interval format. Use "edit attributes" to set chromosome, start, end, and strand columns.
40
41-----
42
43**Screencasts!**
44
45See Galaxy Interval Operation Screencasts_ (right click to open this link in another window).
46
47.. _Screencasts: http://bitbucket.org/galaxy/galaxy-central/wiki/GopsDesc
48
49-----
50
51This operation merges all overlapping intervals into single intervals.
52
53**Example**
54
55.. image:: ../static/operation_icons/gops_merge.gif
56
57</help>
58</tool>
Note: リポジトリブラウザについてのヘルプは TracBrowser を参照してください。