Mercurial > repos > bgruening > deeptools_plot_fingerprint

comparison plotFingerprint.xml @ 3:d0c03d57e471 draft

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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2e8510e4f4015f51f7726de5697ba2de9b4e2f4c
author bgruening
date Wed, 09 Mar 2016 17:56:38 -0500
parents 91b340ca9e92
children b9660f621e82
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2:91b340ca9e92 3:d0c03d57e471
112 <help> 112 <help>
113 <![CDATA[ 113 <![CDATA[
114 114
115 115
116 What it does 116 What it does
117 --------------- 117 ------------
118 118
119 This tool is useful for assessing the strength of a ChIP (i.e. how clearly the enrichment signal can be separated from the background) 119 This tool is useful for assessing the strength of a ChIP (i.e. how clearly the enrichment signal can be separated from the background)
120 and is based on a method described in Diaz et al. (2012) Stat Appl Genet Mol Biol 11(3). 120 and is based on a method described in Diaz et al. (2012) Stat Appl Genet Mol Biol 11(3).
121 121
122 122
123 Output 123 Output
124 --------- 124 ------
125 125
126 The default output is a diagnostic plot (see below for an example and further down for some background information). 126 The default output is a diagnostic plot (see below for an example and further down for some background information).
127 127
128 Optionally, you can obtain the table of raw counts that was used to generate the plot. 128 Optionally, you can obtain the table of raw counts that was used to generate the plot.
129 129
140 140
141 .. image:: $PATH_TO_IMAGES/bamFP_galaxy_output.png 141 .. image:: $PATH_TO_IMAGES/bamFP_galaxy_output.png
142 :width: 600 142 :width: 600
143 :height: 450 143 :height: 450
144 144
145 ----------------------------- 145 -----
146 146
147 Theoretical Background 147 Theoretical Background
148 ---------------------- 148 ----------------------
149 149
150 The tool first samples indexed BAM files and counts all reads overlapping a window (bin) of the specified length. 150 The tool first samples indexed BAM files and counts all reads overlapping a window (bin) of the specified length.