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comparison plotCorrelation.xml @ 5:ae54e08b15d7 draft

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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 8b9cdb8dc4a8fedd2b2286e7afab6529e49a9d22-dirty
author bgruening
date Tue, 22 Dec 2015 13:45:00 -0500
parents e556e34fc12a
children 7cbaaf80dced
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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 of correlation scores between different samples </description> 2 <description>creates a heatmap or scatterplot 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"/>
89 <help> 89 <help>
90 <![CDATA[ 90 <![CDATA[
91 **What it does** 91 **What it does**
92 92
93 This tools takes a compressed matrix of scores (such as read coverages) for a number of genomic regions 93 This tools takes a compressed matrix of scores (such as read coverages) for a number of genomic regions
94 and different samples. It can visualize the correlation among samples as scatterplots or as 94 and different samples. It can visualize the correlation among samples as scatterplots or as
95 heatmap of correlation coefficients. Further output files are optional. 95 heatmap of correlation coefficients. Further output files are optional.
96 The compressed input matrices are easily generated using the "bamCorrelate" and "bigwigCorrelate" modules of deeptools. 96 The compressed input matrices are easily generated using the "bamCorrelate" and "bigwigCorrelate" modules of deeptools.
97 97
98 98
99 .. image:: $PATH_TO_IMAGES/QC_bamCorrelate_humanSamples.png 99 .. image:: $PATH_TO_IMAGES/QC_bamCorrelate_humanSamples.png
103 You can find more details on plotCorrelation here http://deeptools.readthedocs.org/en/release-1.6/content/tools/plotCorrelation.html 103 You can find more details on plotCorrelation here http://deeptools.readthedocs.org/en/release-1.6/content/tools/plotCorrelation.html
104 104
105 105
106 **Output files**: 106 **Output files**:
107 107
108 - **correlation structure**: a scatterplot of all mutual correlations between all samples in matrix 108 - **diagnostic plot**: Either a scatterplot or clustered heatmap (select above) displaying the values for each pair-wise correlation,
109 - **diagnostic plot**: clustered heatmap displaying the values for each pair-wise correlation, see below for an example 109 see below for an example
110 - 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 110 - 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
111
112 **Output with test dataset**:
113
114 Following is the output of plotCorrelation with our test ChIP-Seq datasets. Average coverages were computed over 10kb bins for chromosome X,
115 from bigwig files using bigwigCorrelate. The output was used by plotCorrelation to make a heatmap of spearman correlation between samples.
116
117 .. image:: $PATH_TO_IMAGES/plotCorrelation_galaxy_bw_heatmap_output.png
118
111 119
112 ----- 120 -----
113 121
114 @REFERENCES@ 122 @REFERENCES@
115 ]]> 123 ]]>