Mercurial > repos > mmaiensc > ember
comparison GALAXY_FILES/tools/EMBER/Integrate_Data.xml @ 0:003f802d4c7d
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author | mmaiensc |
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date | Wed, 29 Feb 2012 15:03:33 -0500 |
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1 <tool id="integrate_data" name="Integrate Data" version="1.3"> | |
2 <description>Assigns potential targets to binding sites</description> | |
3 <command interpreter="perl">Integrate_Data.pl -b $binding_data -e $expression_data -o $output -d $dist -dt $dtype -v n</command> | |
4 <inputs> | |
5 <param format="txt" name="binding_data" type="data" label="Binding data"/> | |
6 <param format="txt" name="expression_data" type="data" label="Discretized expression data"/> | |
7 <param name="dist" type="integer" min="0" label="Max distance (kbp)" value="100" optional="true"/> | |
8 <param name="dtype" type="select" label="Distance type"> | |
9 <option value="1" selected="true">To gene boundaries</option> | |
10 <option value="2">To TSS</option> | |
11 </param> | |
12 </inputs> | |
13 <outputs> | |
14 <data format="txt" name="output"/> | |
15 </outputs> | |
16 | |
17 <tests> | |
18 <test> | |
19 <param name="binding_data" value="EMBER/peaks.txt"/> | |
20 <param name="expression_data" value="EMBER/expression_profiles.txt"/> | |
21 <param name="dist" value="100"/> | |
22 <param name="dtype" value="1"/> | |
23 <output name="output" file="EMBER/integrated.txt"/> | |
24 </test> | |
25 </tests> | |
26 | |
27 <help> | |
28 | |
29 This tool combines binding data with annotated gene/probe sets to assign potential targets to each binding site. | |
30 | |
31 ----- | |
32 | |
33 Description of inputs: | |
34 | |
35 *Binding Data*: | |
36 | |
37 Binding data in bed-like format (note only the first coordinate after [chr] is used, so if you have the regular bed format, you may want to add a new second column with the average of the start and end coordinates). [other information] is retained throughout the analysis, and may contain peak ID, peak enrichment, etc. | |
38 | |
39 *Format (at least 2 columns)*: [chr] [peak posn] [other information] | |
40 | |
41 *Discretized Expression Data*: output of PreProcess Expression Data. | |
42 | |
43 *Max Distance*: maximum distance from a peak in order to consider a gene a potential target (in kbp). | |
44 | |
45 *Distance Type*: definition of distance (to gene boundaries or to TSS). If "To gene boundaries" is chosen, peaks lying within a gene's coordinates have a distance of 0. | |
46 | |
47 </help> | |
48 | |
49 </tool> | |
50 |