diff mytools/metaintv.xml @ 7:f0dc65e7f6c0

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mytools/metaintv.xml	Fri Mar 09 19:59:07 2012 -0500
@@ -0,0 +1,36 @@
+<tool id="metaintv" name="binned-average">
+  <description>from bigwig</description>
+  <command interpreter="python">binnedAverage.py $bwfile $intvfile $nbin $outfile $outplot </command>
+  <inputs>
+      <param name="intvfile" format="bed" type="data" label="BED file (require strand in column 6)"/>
+      <param name="bwfile" format="bigwig" type="data" label="BigWig file"/> 
+      <param name="nbin" type="integer" value="20" label="number of bins"/>
+                
+  </inputs>
+  <outputs>
+    <data format="tabular" name="outfile" label="${tool.name} on ${on_string}[data]"/>
+        <data format="pdf" name="outplot" label="${tool.name} on ${on_string}[plot]"/>
+  </outputs>
+  <help>
+
+.. class:: infomark
+
+Each interval is binned and the average base-resolution score/coverage/density in the bigwig file is added as new columns appended at the end of the original file .
+
+**Example**
+
+If your original data has the following format:
+
++-----+-----+---+------+
+|chrom|start|end|other2|
++-----+-----+---+------+
+
+and you choose to divide each interval into 3 bins and return the mean scores of each bin, your output will look like this:
+
++-----+-----+---+------+-----+-----+-----+
+|chrom|start|end|other2|mean1|mean2|mean3|
++-----+-----+---+------+-----+-----+-----+
+
+
+</help>
+</tool>