Mercurial > repos > bgruening > deeptools_plot_correlation

comparison plotCorrelation.xml @ 0:bfa132aacee6 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 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
author bgruening
date Mon, 25 Jan 2016 20:22:46 -0500
parents
children 0ed13872209b
comparison
equal deleted inserted replaced
-1:000000000000 0:bfa132aacee6
1 <tool id="deeptools_plot_correlation" name="plotCorrelation" version="@WRAPPER_VERSION@.0">
2 <description>creates a heatmap or scatterplot of correlation scores between different samples </description>
3 <macros>
4 <token name="@BINARY@">plotCorrelation</token>
5 <import>deepTools_macros.xml</import>
6 </macros>
7 <expand macro="requirements"/>
8 <command>
9 <![CDATA[
10 @BINARY@
11 --corData "$corData"
12 --plotFile "$outFileName"
13 --corMethod "$corMethod"
14 --whatToPlot "$plotting_type.whatToPlot"
15 #if str($plotting_type.whatToPlot) == 'heatmap':
16 @HEATMAP_OPTIONS@
17 #else:
18 --plotTitle '$plotting_type.plotTitle'
19 #end if
20 $skipZeros
21 --plotFileFormat "$outFileFormat"
22 $removeOutliers
23 #if $outFileCorMatrix:
24 --outFileCorMatrix "$matrix"
25 #end if
26
27 ]]>
28 </command>
29 <inputs>
30 <param name="corData" format="deeptools_coverage_matrix" type="data" label="Matrix file from the multiBamSummary tool"/>
31 <expand macro="corMethod" />
32
33 <conditional name="plotting_type" >
34 <param argument="--whatToPlot" type="select" label="Plotting type">
35 <option value="heatmap" selected="True">Heatmap</option>
36 <option value="scatterplot">Scatterplot</option>
37 </param>
38 <when value="heatmap">
39 <expand macro="heatmap_options" />
40 </when>
41 <when value="scatterplot">
42 <expand macro="plotTitle" />
43 </when>
44 </conditional>
45
46 <expand macro="skipZeros" />
47
48 <expand macro="input_image_file_format" />
49
50 <param argument="--removeOutliers" type="boolean"
51 truevalue="--removeOutliers" falsevalue="" label="Remove regions with very large counts"
52 help="If set, bins with very large counts are removed. Bins
53 with abnormally high reads counts artificially
54 increase pearson correlation; that's why, by default,
55 plotCorrelation tries to remove outliers using the median
56 absolute deviation (MAD) method applying a threshold
57 of 200 to only consider extremely large deviations
58 from the median. ENCODE blacklist page (https://sites.
59 google.com/site/anshulkundaje/projects/blacklists)
60 contains useful information about regions with
61 unusually high counts."/>
62
63 <param name="outFileCorMatrix" type="boolean" label="Save the matrix of values underlying the heatmap"/>
64
65 </inputs>
66 <outputs>
67 <expand macro="output_image_file_format_not_nested" />
68 <data format="tabular" name="matrix" label="${tool.name} on ${on_string}: Correlation matrix">
69 <filter>outFileCorMatrix is True</filter>
70 </data>
71 </outputs>
72 <tests>
73 <test>
74 <param name="corData" value="multiBamSummary_result1.npz" ftype="deeptools_coverage_matrix" />
75 <param name="outFileFormat" value="png" />
76 <param name="outFileCorMatrix" value="True" />
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" />
79 </test>
80 <test>
81 <param name="corData" value="multiBamSummary_result1.npz" ftype="deeptools_coverage_matrix" />
82 <param name="outFileFormat" value="png" />
83 <param name="whatToPlot" value="scatterplot" />
84 <param name="removeOutliers" value="True" />
85 <param name="plotTitle" value="Test Plot" />
86 <output name="outFileName" file="plotCorrelation_result2.png" ftpye="png" compare="sim_size" delta="100" />
87 </test>
88 </tests>
89 <help>
90 <![CDATA[
91 **What it does**
92
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
95 a heatmap of correlation coefficients. Further output files are optional.
96 The compressed input matrices are easily generated using the "multiBamSummary" and "multiBigwigSummary" tools.
97
98
99 .. image:: $PATH_TO_IMAGES/QC_multiBamSummary_humanSamples.png
100 :alt: Heatmap of RNA Polymerase II ChIP-seq
101
102
103 You can find more details on plotCorrelation here http://deeptools.readthedocs.org/en/master/content/tools/plotCorrelation.html
104
105
106 **Output files**:
107
108 - **diagnostic plot**: Either a scatterplot or clustered heatmap (select above) displaying the values for each pair-wise correlation,
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
111
112 **Output with test dataset**:
113
114 The 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 multiBigwigSummary. 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
119
120 -----
121
122 @REFERENCES@
123 ]]>
124 </help>
125 <expand macro="citations" />
126 </tool>