diff heatmapper.xml @ 6:c5847db0cb41 draft

Uploaded

--- a/heatmapper.xml	Tue Aug 06 08:20:47 2013 -0400
+++ b/heatmapper.xml	Wed Aug 14 07:18:18 2013 -0400
@@ -1,4 +1,4 @@
-<tool id="heatmapper" name="Heatmapper" version="1.0">
+<tool id="deeptools_heatmapper" name="heatmapper" version="1.0">
   <description>creates a heatmap for a score associated to genomic regions</description>
 
   <requirements>
@@ -7,7 +7,8 @@
     <requirement type="package" version="1.2.1">matplotlib</requirement>
     <requirement type="package" version="0.12.0">scipy</requirement>
     <requirement type="package" version="0.1">ucsc_tools</requirement>
-    <requirement type="package" version="1.5.1_59e067cce039cb93add04823c9f51cab202f8c2b">deepTools</requirement>
+    <requirement type="package" version="1.5.1_df852fa1ef13251a17274ee18fbf919fbc515079">deepTools</requirement>
+    <requirement type="package" >deepTools</requirement>
   </requirements>
 
   <command>
@@ -119,8 +120,8 @@
       <when value="yes">
         <param name="sortRegions" type="select" label="Sort regions"
            help="Whether the heatmap should present the regions sorted. The default is to sort in descending order based on the mean value per region.">
-          <option value="no" selected="true">no ordering</option>
-          <option value="descend">descending order</option>
+          <option value="no">no ordering</option>
+          <option value="descend" selected="true">descending order</option>
           <option value="ascend">ascending order</option>
         </param>
 
@@ -347,19 +348,19 @@
 
 **What it does**
 
-HeatMapper visualizes scores associated with genomic regions, for example  log2 fold change values obtained from ChIP-seq experiments. Those values can be visualized individually along  each of the regions provided by the user.
+The heatmapper visualizes scores associated with genomic regions, for example ChIP enrichment values around the TSS of genes. Those values can be visualized individually along each of the regions provided by the user in INTERVAL or BED format. In addition to the heatmap, an average profile plot is plotted on top of the heatmap (can be turned off by the user; it can also be generated separately by the tool profiler). We implemented vast optional parameters and we encourage you to play around with the min/max values displayed in the heatmap as well as with the different coloring options. If you would like to plot heatmaps for different groups of genomic regions individually, e.g. one plot per chromosome, simply supply each group as an individual BED file.
 
 -----
 
 .. class:: infomark
 
-If you would like to give us feedback or you run into any trouble, please sent an email to [e-mail]
+If you would like to give us feedback or you run into any trouble, please send an email to [e-mail]
 
 This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_.
 
 
 .. _Bioinformatics and Deep-Sequencing Unit: http://www3.ie-freiburg.mpg.de/facilities/research-facilities/bioinformatics-and-deep-sequencing-unit/
 .. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de
-.. _Fidel Ramirez: [e-mail]
+
   </help>
 </tool>