Mercurial > repos > mmaiensc > ember
diff GALAXY_FILES/tools/EMBER/Integrate_Data.xml @ 3:037c3edda16e
Uploaded
author | mmaiensc |
---|---|
date | Thu, 22 Mar 2012 13:49:52 -0400 |
parents | |
children |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/GALAXY_FILES/tools/EMBER/Integrate_Data.xml Thu Mar 22 13:49:52 2012 -0400 @@ -0,0 +1,50 @@ +<tool id="integrate_data" name="Integrate Data" version="1.3.1"> + <description>Step 2 of analysis: assigns potential targets to binding sites</description> + <command interpreter="perl">Integrate_Data.pl -b $binding_data -e $expression_data -o $output -d $dist -dt $dtype -v n</command> + <inputs> + <param format="txt" name="binding_data" type="data" label="Binding data"/> + <param format="txt" name="expression_data" type="data" label="Discretized expression data"/> + <param name="dist" type="integer" min="0" label="Max distance (kbp)" value="100" optional="true"/> + <param name="dtype" type="select" label="Distance type"> + <option value="1" selected="true">To gene boundaries</option> + <option value="2">To TSS</option> + </param> + </inputs> + <outputs> + <data format="txt" name="output"/> + </outputs> + + <tests> + <test> + <param name="binding_data" value="EMBER/peaks.txt"/> + <param name="expression_data" value="EMBER/expression_profiles.txt"/> + <param name="dist" value="100"/> + <param name="dtype" value="1"/> + <output name="output" file="EMBER/integrated.txt"/> + </test> + </tests> + + <help> + +This tool combines binding data with annotated gene/probe sets to assign potential targets to each binding site. + +----- + +Description of inputs: + +*Binding Data*: + + 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. + + *Format (at least 2 columns)*: [chr] [peak posn] [other information] + +*Discretized Expression Data*: output of PreProcess Expression Data. + +*Max Distance*: maximum distance from a peak in order to consider a gene a potential target (in kbp). + +*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. + + </help> + +</tool> +