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annotate merge.xml @ 4:a2f62c0c0537 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/merge commit de7140295cce07e1bc1697e51dab4271c8d7a8a6
author | devteam |
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date | Fri, 18 Dec 2015 19:39:00 -0500 |
parents | 1e9d95cae35f |
children | dfbbc0291b36 |
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1
72e1fdd8e7ae
Corrected version string.
devteam <devteam@galaxyproject.org>
parents:
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1 <tool id="gops_merge_1" name="Merge" version="1.0.0"> |
0 | 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 | |
2 | 59 .. image:: gops_merge.gif |
0 | 60 |
61 </help> | |
62 </tool> |