comparison tools/new_operations/complement.xml @ 0:9071e359b9a3

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author xuebing
date Fri, 09 Mar 2012 19:37:19 -0500
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1 <tool id="gops_complement_1" name="Complement">
2 <description>intervals of a dataset</description>
3 <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>
4 <inputs>
5 <param format="interval" name="input1" type="data">
6 <label>Complement regions of</label>
7 </param>
8 <param name="allchroms" type="boolean" truevalue="--all" falsevalue="" label="Genome-wide complement">
9 </param>
10 </inputs>
11 <outputs>
12 <data format="input" name="output" metadata_source="input1" />
13 </outputs>
14 <code file="operation_filter.py"/>
15 <tests>
16 <test>
17 <param name="input1" value="1.bed" dbkey="?" />
18 <param name="allchroms" value="true" />
19 <output name="output" file="gops_complement_out.bed" />
20 </test>
21 <test>
22 <param name="input1" value="2_mod.bed" ftype="interval" dbkey="?" />
23 <param name="allchroms" value="true" />
24 <output name="output" file="gops_complement_out_diffCols.dat" />
25 </test>
26 <test>
27 <param name="input1" value="gops_bigint.interval" dbkey="?" />
28 <param name="allchroms" value="true" />
29 <output name="output" file="gops_complement_out2.bed" />
30 </test>
31 </tests>
32 <help>
33
34 .. class:: infomark
35
36 **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.
37
38 This operation complements the regions of a set of intervals. Regions are returned that represent the empty space in the input interval.
39
40 -----
41
42 **Screencasts!**
43
44 See Galaxy Interval Operation Screencasts_ (right click to open this link in another window).
45
46 .. _Screencasts: http://wiki.g2.bx.psu.edu/Learn/Interval%20Operations
47
48 -----
49
50 **Syntax**
51
52 - **Genome-wide complement** will complement all chromosomes of the genome. Leaving this option unchecked will only complement chromosomes present in the dataset.
53
54 -----
55
56 **Example**
57
58 .. image:: ./static/operation_icons/gops_complement.gif
59
60 </help>
61 </tool>