# HG changeset patch
# User greg
# Date 1503415329 14400
# Node ID 859687afe7bc86f436c0821a3fd38b4f14a808d6
# Parent  b287aae59e1d6f97dac6acf99b75c51d589b433a
Uploaded

diff -r b287aae59e1d -r 859687afe7bc ideas.xml
--- a/ideas.xml	Tue Aug 22 11:09:28 2017 -0400
+++ b/ideas.xml	Tue Aug 22 11:22:09 2017 -0400
@@ -168,7 +168,10 @@
             <when value="no"/>
             <when value="yes"/>
         </conditional>
-        <param name="reads_per_bp" type="integer" value="1" min="1" max="8" label="Number of reads per base pair for calculating the average signal in each genomic window"/>
+        <param name="reads_per_bp" type="select" display="radio" label="Calculate the average signal in each genomic window using">
+            <option value="6" selected="true">mean</option>
+            <option value="8">max</option>
+        </param>
         <param name="blacklist_input" type="data" format="bed" optional="True" multiple="True" label="Select file(s) containing regions to exclude"/>
         <conditional name="standardize_datasets_cond">
             <param name="standardize_datasets" type="select" display="radio" label="Standardize all datasets">
@@ -240,6 +243,7 @@
 **Other options**
 
 * **Output chromosomes in seperate files** - select "Yes" to produce seperate files for each chromosome, allowing you to run IDEAS on different chromosomes separately.
+* **Calculate the average signal in each genomic window using** - use the bigWigAverageOverBed utility from the UCSC genome browser to calculate average signal (number of reads per bp) in each genomic window.
 * **Select file(s) containing regions to exclude** - select one or more bed files that contains regions you'd like excluded from your datasets.
 * **Standardize all datasets** - select "Yes" to standardize all datasets (e.g., reads / total_reads * 20 million) so that the signals from different cell types become comparable - your datasets can be read counts, logp-values or fold change.