comparison merge.xml @ 0:b488a1fa07f6

Imported from capsule None
author devteam
date Tue, 01 Apr 2014 10:53:37 -0400
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children 55e88307811d
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-1:000000000000 0:b488a1fa07f6
1 <tool id="gops_merge_1" name="Merge">
2 <description>the overlapping intervals of a dataset</description>
3 <requirements>
4 <requirement type="package" version="0.7.1">bx-python</requirement>
5 <requirement type="package" version="1.0.0">galaxy-ops</requirement>
6 </requirements>
7 <command interpreter="python">gops_merge.py $input1 $output -1 ${input1.metadata.chromCol},${input1.metadata.startCol},${input1.metadata.endCol},${input1.metadata.strandCol} $returntype</command>
8 <inputs>
9 <param format="interval" name="input1" type="data">
10 <label>Merge overlaping regions of</label>
11 </param>
12 <param name="returntype" type="boolean" truevalue="-3" falsevalue="">
13 <label>Output 3 column bed</label>
14 </param>
15 </inputs>
16 <outputs>
17 <data format="input" name="output" metadata_source="input1" />
18 </outputs>
19 <code file="operation_filter.py">
20 <hook exec_after_process="exec_after_merge" />
21 </code>
22 <tests>
23 <test>
24 <param name="input1" value="1.bed" />
25 <output name="output" file="gops-merge.dat" />
26 <param name="returntype" value="true" />
27 </test>
28 <test>
29 <param name="input1" value="2_mod.bed" ftype="interval"/>
30 <output name="output" file="gops_merge_diffCols.dat" />
31 <param name="returntype" value="true" />
32 </test>
33 <test>
34 <param name="input1" value="gops_bigint.interval" />
35 <output name="output" file="gops_merge_out2.bed" />
36 <param name="returntype" value="true" />
37 </test>
38 </tests>
39 <help>
40
41 .. class:: infomark
42
43 **TIP:** If your dataset 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.
44
45 -----
46
47 **Screencasts!**
48
49 See Galaxy Interval Operation Screencasts_ (right click to open this link in another window).
50
51 .. _Screencasts: http://wiki.g2.bx.psu.edu/Learn/Interval%20Operations
52
53 -----
54
55 This operation merges all overlapping intervals into single intervals.
56
57 **Example**
58
59 .. image:: ${static_path}/operation_icons/gops_merge.gif
60
61 </help>
62 </tool>