Mercurial > repos > bgruening > deeptools_plot_correlation

comparison plotCorrelation.xml @ 11:cc0acb70ded3 draft

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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee
author bgruening
date Mon, 25 Jan 2016 14:10:43 -0500
parents 59ca699c7b77
children 49ac0d30a800
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10:12898c0f81b7 11:cc0acb70ded3
25 #end if 25 #end if
26 26
27 ]]> 27 ]]>
28 </command> 28 </command>
29 <inputs> 29 <inputs>
30 <param name="corData" format="deeptools_coverage_matrix" type="data" label="Matrix file from the multiBamCoverage tool"/> 30 <param name="corData" format="deeptools_coverage_matrix" type="data" label="Matrix file from the multiBamSummary tool"/>
31 <expand macro="corMethod" /> 31 <expand macro="corMethod" />
32 32
33 <conditional name="plotting_type" > 33 <conditional name="plotting_type" >
34 <param argument="--whatToPlot" type="select" label="Plotting type"> 34 <param argument="--whatToPlot" type="select" label="Plotting type">
35 <option value="heatmap" selected="True">Heatmap</option> 35 <option value="heatmap" selected="True">Heatmap</option>
69 <filter>outFileCorMatrix is True</filter> 69 <filter>outFileCorMatrix is True</filter>
70 </data> 70 </data>
71 </outputs> 71 </outputs>
72 <tests> 72 <tests>
73 <test> 73 <test>
74 <param name="corData" value="multiBamCoverage_result1.npz" ftype="deeptools_coverage_matrix" /> 74 <param name="corData" value="multiBamSummary_result1.npz" ftype="deeptools_coverage_matrix" />
75 <param name="outFileFormat" value="png" /> 75 <param name="outFileFormat" value="png" />
76 <param name="outFileCorMatrix" value="True" /> 76 <param name="outFileCorMatrix" value="True" />
77 <output name="matrix" file="plotCorrelation_result1.tabular" ftype="tabular" /> 77 <output name="matrix" file="plotCorrelation_result1.tabular" ftype="tabular" />
78 <output name="outFileName" file="plotCorrelation_result1.png" ftype="png" compare="sim_size" delta="100" /> 78 <output name="outFileName" file="plotCorrelation_result1.png" ftype="png" compare="sim_size" delta="100" />
79 </test> 79 </test>
80 <test> 80 <test>
81 <param name="corData" value="multiBamCoverage_result1.npz" ftype="deeptools_coverage_matrix" /> 81 <param name="corData" value="multiBamSummary_result1.npz" ftype="deeptools_coverage_matrix" />
82 <param name="outFileFormat" value="png" /> 82 <param name="outFileFormat" value="png" />
83 <param name="whatToPlot" value="scatterplot" /> 83 <param name="whatToPlot" value="scatterplot" />
84 <param name="removeOutliers" value="True" /> 84 <param name="removeOutliers" value="True" />
85 <param name="plotTitle" value="Test Plot" /> 85 <param name="plotTitle" value="Test Plot" />
86 <output name="outFileName" file="plotCorrelation_result2.png" ftpye="png" compare="sim_size" delta="100" /> 86 <output name="outFileName" file="plotCorrelation_result2.png" ftpye="png" compare="sim_size" delta="100" />
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 a heatmap of correlation coefficients. Further output files are optional. 95 a heatmap of correlation coefficients. Further output files are optional.
96 The compressed input matrices are easily generated using the "multiBamCoverage" and "multiBigwigSummary" tools. 96 The compressed input matrices are easily generated using the "multiBamSummary" and "multiBigwigSummary" tools.
97 97
98 98
99 .. image:: $PATH_TO_IMAGES/QC_multiBamCoverage_humanSamples.png 99 .. image:: $PATH_TO_IMAGES/QC_multiBamSummary_humanSamples.png
100 :alt: Heatmap of RNA Polymerase II ChIP-seq 100 :alt: Heatmap of RNA Polymerase II ChIP-seq
101 101
102 102
103 You can find more details on plotCorrelation here http://deeptools.readthedocs.org/en/master/content/tools/plotCorrelation.html 103 You can find more details on plotCorrelation here http://deeptools.readthedocs.org/en/master/content/tools/plotCorrelation.html
104 104