Mercurial > repos > bgruening > deeptools_plot_correlation

comparison plotCorrelation.xml @ 2:c5634baf9bf9 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4e5124484b42d4ffef76af4bd82a6feb67a5b829
author bgruening
date Fri, 18 Dec 2015 12:27:26 -0500
parents b0050909cf03
children e556e34fc12a
comparison
equal deleted inserted replaced
1:08b01bdab227 2:c5634baf9bf9
1 <tool id="deeptools_plot_correlation" name="plotCorrelation" version="@WRAPPER_VERSION@.0"> 1 <tool id="deeptools_plot_correlation" name="plotCorrelation" version="@WRAPPER_VERSION@.0">
2 <description>creates a heatmap for a score associated to genomic regions</description> 2 <description>creates a heatmap of correlation scores between different samples </description>
3 <macros> 3 <macros>
4 <token name="@BINARY@">plotCorrelation</token> 4 <token name="@BINARY@">plotCorrelation</token>
5 <import>deepTools_macros.xml</import> 5 <import>deepTools_macros.xml</import>
6 </macros> 6 </macros>
7 <expand macro="requirements"/> 7 <expand macro="requirements"/>
23 <inputs> 23 <inputs>
24 <param name="corData" format="deeptools_coverage_matrix" type="data" label="Matrix file from the bamCorrelate tool"/> 24 <param name="corData" format="deeptools_coverage_matrix" type="data" label="Matrix file from the bamCorrelate tool"/>
25 <expand macro="corMethod" /> 25 <expand macro="corMethod" />
26 26
27 <param argument="--whatToPlot" type="select" label="Plotting type"> 27 <param argument="--whatToPlot" type="select" label="Plotting type">
28 <option value="heatmap" selected="True">Spearman</option> 28 <option value="heatmap" selected="True">Heatmap</option>
29 <option value="scatterplot">Pearson</option> 29 <option value="scatterplot">Scatterplot</option>
30 </param> 30 </param>
31 31
32 <expand macro="skipZeros" /> 32 <expand macro="skipZeros" />
33 33
34 <expand macro="image_file_format" /> 34 <expand macro="image_file_format" />
75 </tests> 75 </tests>
76 <help> 76 <help>
77 <![CDATA[ 77 <![CDATA[
78 **What it does** 78 **What it does**
79 79
80 Tool for visualizing a correlation using either bamCorrelate or 80 This tools takes a compressed matrix of scores (such as read coverages) for a number of genomic regions
81 bigwigCorrelate. Pearson or Spearman methods are available to compute correlation 81 and different samples. It can visualize the correlation among samples as scatterplots or as
82 coefficients. Results can be saved into a heat map image or as multiple 82 heatmap of correlation coefficients. Further output files are optional.
83 scatter plots. Further output files are optional. 83 The compressed input matrices are easily generated using the "bamCorrelate" and "bigwigCorrelate" modules of deeptools.
84
85
86 .. image:: $PATH_TO_IMAGES/QC_bamCorrelate_humanSamples.png
87 :alt: Heatmap of RNA Polymerase II ChIP-seq
88
89
90 You can find more details on plotCorrelation here http://deeptools.readthedocs.org/en/release-1.6/content/tools/plotCorrelation.html
91
92
93 **Output files**:
94
95 - **correlation structure**: a scatterplot of all mutual correlations between all samples in matrix
96 - **diagnostic plot**: clustered heatmap displaying the values for each pair-wise correlation, see below for an example
97 - data matrix (optional): if you want to analyze or plot the correlation values using a different program, e.g. R, this matrix can be used
84 98
85 ----- 99 -----
86 100
87 @REFERENCES@ 101 @REFERENCES@
88 ]]> 102 ]]>