Mercurial > repos > devteam > complement
annotate complement.xml @ 2:2221cf5f59aa
Added tool image.
author | Dave Bouvier <dave@bx.psu.edu> |
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date | Mon, 14 Apr 2014 12:34:29 -0400 |
parents | 67c4ed724bfd |
children | 38c8bb402872 |
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67c4ed724bfd
Corrected version string.
devteam <devteam@galaxyproject.org>
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1 <tool id="gops_complement_1" name="Complement" version="1.0.0"> |
0 | 2 <description>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_complement.py $input1 $output -1 ${input1.metadata.chromCol},${input1.metadata.startCol},${input1.metadata.endCol},${input1.metadata.strandCol} -l ${chromInfo} $allchroms</command> | |
8 <inputs> | |
9 <param format="interval" name="input1" type="data"> | |
10 <label>Complement regions of</label> | |
11 </param> | |
12 <param name="allchroms" type="boolean" truevalue="--all" falsevalue="" label="Genome-wide complement"> | |
13 </param> | |
14 </inputs> | |
15 <outputs> | |
16 <data format="input" name="output" metadata_source="input1" /> | |
17 </outputs> | |
18 <code file="operation_filter.py"/> | |
19 <tests> | |
20 <test> | |
21 <param name="input1" value="1.bed" dbkey="hg17" /> | |
22 <param name="allchroms" value="true" /> | |
23 <output name="output" file="gops_complement_out.bed" /> | |
24 </test> | |
25 <test> | |
26 <param name="input1" value="2_mod.bed" ftype="interval" dbkey="hg17" /> | |
27 <param name="allchroms" value="true" /> | |
28 <output name="output" file="gops_complement_out_diffCols.dat" /> | |
29 </test> | |
30 <test> | |
31 <param name="input1" value="gops_bigint.interval" dbkey="hg17" /> | |
32 <param name="allchroms" value="true" /> | |
33 <output name="output" file="gops_complement_out2.bed" /> | |
34 </test> | |
35 </tests> | |
36 <help> | |
37 | |
38 .. class:: infomark | |
39 | |
40 **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. | |
41 | |
42 This operation complements the regions of a set of intervals. Regions are returned that represent the empty space in the input interval. | |
43 | |
44 ----- | |
45 | |
46 **Screencasts!** | |
47 | |
48 See Galaxy Interval Operation Screencasts_ (right click to open this link in another window). | |
49 | |
50 .. _Screencasts: http://wiki.g2.bx.psu.edu/Learn/Interval%20Operations | |
51 | |
52 ----- | |
53 | |
54 **Syntax** | |
55 | |
56 - **Genome-wide complement** will complement all chromosomes of the genome. Leaving this option unchecked will only complement chromosomes present in the dataset. | |
57 | |
58 ----- | |
59 | |
60 **Example** | |
61 | |
2 | 62 .. image:: gops_complement.gif |
0 | 63 |
64 </help> | |
65 </tool> |