diff plotFingerprint.xml @ 1:a6d0ddc266bf draft

planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920

--- a/plotFingerprint.xml	Mon Jan 25 20:15:58 2016 -0500
+++ b/plotFingerprint.xml	Mon Feb 15 10:26:21 2016 -0500
@@ -113,11 +113,40 @@
 <![CDATA[
 
 
-**What it does**
+What it does
+---------------
 
 This tool is useful for assessing the strength of a ChIP (i.e. how clearly the enrichment signal can be separated from the background)
 and is based on a method described in Diaz et al. (2012) Stat Appl Genet Mol Biol 11(3).
 
+
+Output
+---------
+
+The default output is a diagnostic plot (see below for an example and further down for some background information).
+
+Optionally, you can obtain the table of raw counts that was used to generate the plot.
+
+.. image:: $PATH_TO_IMAGES/plotFingerprint_output.png
+  :width: 600
+  :height: 395
+
+
+Example plot
+-------------
+
+What follows is the output of ``plotFingerprint`` with our test ChIP-Seq data sets, limiting the analysis to chromosome X. Single-end reads were extended to
+200 bp (advanced options).
+
+.. image:: $PATH_TO_IMAGES/bamFP_galaxy_output.png
+   :width: 600
+   :height: 450
+
+-----------------------------
+
+Background
+--------------
+
 The tool first samples indexed BAM files and counts all reads overlapping a window (bin) of the specified length.
 These counts are then sorted according to their rank (the bin with the highest number of reads has the highest rank)
 and the cumulative sum of read counts are plotted. An ideal input (control) with a uniform distribution of reads alignments
@@ -127,23 +156,8 @@
 
 
 .. image:: $PATH_TO_IMAGES/QC_fingerprint.png
-
-
-You can find more details on the plotFingerprint doc page: https://deeptools.readthedocs.org/en/master/content/tools/plotFingerprint.html
-
-
-**Output files**:
-
-- Diagnostic plot
-- (optional) Data matrix of raw counts
-
-**Output with test dataset**:
-
-What follows is the output of plotFingerprint with our test ChIP-Seq datasets, limiting analysis to chromosome X. Single-end reads were extended to
-200 bp (advanced options).
-
-.. image:: $PATH_TO_IMAGES/bamFP_galaxy_output.png
-
+   :width: 600
+   :height: 294
 
 -----