diff GALAXY_FILES/tools/PreProcess_Expression_Data.xml @ 1:e62b2ba92070 default tip

Uploaded

--- a/GALAXY_FILES/tools/PreProcess_Expression_Data.xml	Wed Feb 29 14:46:05 2012 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,76 +0,0 @@
-<tool id="prep_data" name="PreProcess Expression Data" version="1.3">
-  <description>Combines gene expression data</description>
-  <command interpreter="perl">PreProcess_Expression_Data.pl -i $data -c $compslist -a $annot -o $output -p $thresh -l $log -v n</command>
-  <inputs>
-    <param format="txt" name="data" type="data" label="Expression data"/>
-    <param format="txt" name="compslist" type="data" label="Comparison list"/>
-    <param format="txt" name="annot" type="data" label="Annotation file"/>
-    <param name="thresh" type="float" min="0" max="1" label="Percentile threshold" value="0.63" optional="true"/>
-    <param name="log" type="select" label="Log transform data?">
-        <option value="n" selected="true">No</option>
-        <option value="y">Yes</option>
-    </param>
-  </inputs>
-  <outputs>
-    <data format="txt" name="output"/>
-  </outputs>
-
-  <tests>
-    <test>
-      <param name="data" value="EMBER/expression.txt"/>
-      <param name="compslist" value="EMBER/comparisons_list.txt"/>
-      <param name="annot" value="EMBER/annotation.txt"/>
-      <param name="thresh" value="0.63"/>
-      <param name="log" value="n"/>
-      <output name="output" file="EMBER/expression_profiles.txt"/>
-    </test>
-  </tests>
-
-  <help>
-
-This tool discretizes the gene expression data and adds genomic annotations.
-
-More options for the EMBER tools (especially for the main program, EMBER, including searching for multiple expression patterns) are available in the command line version, available at http://dinner-group.uchicago.edu/downloads.html. That package also includes test data and sample outputs.
-
-When using any of the EMBER tools, please cite: M Maienschein-Cline, J Zhou, KP White, R Sciammas, and AR Dinner. Discovering transcription factor regulatory targets using gene expression and binding data. *Bioinformatics*, 28:206-213 (2012).
-
------
-
-Description of inputs:
-
-*Expression Data*:
-
-   Microarray data, with data from N experiments (and at least 2 replicates per condition).
-   
-   *Format (N+1 columns)*: [ID] [expt 1 value] [expt 2 value] ... [expt N value]
-
-   IMPORTANT: the first line should be a title line, first field "#ID", and subsequent fields giving the condition/replicate for each column, i.e.,
-
-      #ID [condition]#[replicate]...
-
-   where [condition] matches the values in the Comparison List, and replicate tells which number the file is. [condition] and [replicate] are delimited by a "#" (so don't use that character in the condition name).
-
-*Comparison List*:
-
-   List of behavior dimension definitions. [condition] should match the names in the expression data list.
-
-   *Format (2 columns)*: [condition1] [condition2]
-
-*Annotation File*:
-
-   Gives the genomic coordinates of each probe set.
-
-   *Format (6 columns)*: [probe id] [gene name] [chromosome] [start] [end] [strand]
-
-*Percentile Threshold* (p):
-
-   Used to eliminate genes that are consistently expressed at a very low level. All data are concatenated into one list, and the pth percentile of that list is taken as the thresold. Then a probe set is removed if its value is less than the threshold in ALL conditions.
-
-   p = 1.0 means all probes are retained, p = 0.0 means none are. However, note that this does NOT necessarily imply that 0.63 means 63% of probe sets are retained.
-
-*Log Transform*: whether or not to take the log of the data before discretization.
-
-  </help>
-
-</tool>
-