diff bamFingerprint.xml @ 8:ab153e5b5428 draft default tip

planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4f515024772311c950d277246db548453d24abd7

--- a/bamFingerprint.xml	Wed Dec 23 07:31:18 2015 -0500
+++ b/bamFingerprint.xml	Wed Dec 23 14:40:57 2015 -0500
@@ -58,8 +58,8 @@
             <when value="no" />
             <when value="yes">
                 <param argument="--binSize" type="integer" value="500" min="1"
-                   label="Bin size in bp"
-                   help="Length in base pairs for a window used to sample the genome."/>
+                   label="Bin size in bases"
+                   help="Length in bases for a window used to sample the genome."/>
                 <param argument="--numberOfSamples" type="integer" value="100000" min="1"
                    label="Number of samples"
                    help="Number of samples taken from the genome to compute the scaling factors."/>
@@ -115,16 +115,15 @@
 
 **What it does**
 
-This tool is useful to assess the strength of a ChIP (i.e. how clearly the enrichment signal can be separated from the background signal)
-and it is based on a method developed by Diaz et al. (2012) Stat Appl Genet Mol Biol 11(3).
+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).
 
-The tool first samples indexed BAM files and counts all reads overlapping a window (bin) of specified length.
+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 sample) with perfect uniform distribution of reads
-along the genome (i.e. without enrichments in open chromatin etc.) should
-generate a straight diagonal line. A very specific and strong ChIP enrichment will be indicated by a prominent and steep
-rise of the cumulative sum towards the highest rank. This means that a big chunk of reads from the ChIP sample is located in
-few bins which corresponds to high, narrow enrichments seen for transcription factors.
+and the cumulative sum of read counts are plotted. An ideal input (control) with a uniform distribution of reads alignments
+result in a diagonal line. A very specific and strong ChIP enrichment, on the other hand, would result in a large portion
+of reads accumulating in just a few bins and the resulting plot showing a steep rise toward the right-most edge. Such results are
+most commonly seen with transcription factors.
 
 
 .. image:: $PATH_TO_IMAGES/QC_fingerprint.png
@@ -140,7 +139,7 @@
 
 **Output with test dataset**:
 
-Following is the output of bamFingerPrint with our test ChIP-Seq datasets, limiting analysis to chromosome X. Single-end reads were extended to
+What follows is the output of bamFingerPrint 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