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comparison GALAXY_FILES/tools/EMBER/Integrate_Data.xml @ 0:003f802d4c7d

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author mmaiensc
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