Mercurial > repos > bgruening > deeptools_plot_correlation

comparison plotCorrelation.xml @ 3:e556e34fc12a draft

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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f
author bgruening
date Mon, 21 Dec 2015 07:24:37 -0500
parents c5634baf9bf9
children ae54e08b15d7
comparison
equal deleted inserted replaced
2:c5634baf9bf9 3:e556e34fc12a
9 <![CDATA[ 9 <![CDATA[
10 @BINARY@ 10 @BINARY@
11 --corData "$corData" 11 --corData "$corData"
12 --plotFile "$outFileName" 12 --plotFile "$outFileName"
13 --corMethod "$corMethod" 13 --corMethod "$corMethod"
14 --whatToPlot "$whatToPlot" 14 --whatToPlot "$plotting_type.whatToPlot"
15 #if str($plotting_type.whatToPlot) == 'heatmap':
16 @HEATMAP_OPTIONS@
17 #else:
18 --plotTitle '$plotting_type.plotTitle'
19 #end if
15 $skipZeros 20 $skipZeros
16 --plotFileFormat "$outFileFormat" 21 --plotFileFormat "$outFileFormat"
17 $removeOutliers 22 $removeOutliers
18 --outFileCorMatrix "$matrix" 23 #if $outFileCorMatrix:
19 @HEATMAP_OPTIONS@ 24 --outFileCorMatrix "$matrix"
25 #end if
20 26
21 ]]> 27 ]]>
22 </command> 28 </command>
23 <inputs> 29 <inputs>
24 <param name="corData" format="deeptools_coverage_matrix" type="data" label="Matrix file from the bamCorrelate tool"/> 30 <param name="corData" format="deeptools_coverage_matrix" type="data" label="Matrix file from the bamCorrelate tool"/>
25 <expand macro="corMethod" /> 31 <expand macro="corMethod" />
26 32
27 <param argument="--whatToPlot" type="select" label="Plotting type"> 33 <conditional name="plotting_type" >
28 <option value="heatmap" selected="True">Heatmap</option> 34 <param argument="--whatToPlot" type="select" label="Plotting type">
29 <option value="scatterplot">Scatterplot</option> 35 <option value="heatmap" selected="True">Heatmap</option>
30 </param> 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>
31 45
32 <expand macro="skipZeros" /> 46 <expand macro="skipZeros" />
33 47
34 <expand macro="image_file_format" /> 48 <expand macro="input_image_file_format" />
35 49
36 <param argument="--removeOutliers" type="boolean" 50 <param argument="--removeOutliers" type="boolean"
37 truevalue="--removeOutliers" falsevalue="" label="Remove regions with very large counts" 51 truevalue="--removeOutliers" falsevalue="" label="Remove regions with very large counts"
38 help="If set, bins with very large counts are removed. Bins 52 help="If set, bins with very large counts are removed. Bins
39 with abnormally high reads counts artificially 53 with abnormally high reads counts artificially
45 google.com/site/anshulkundaje/projects/blacklists) 59 google.com/site/anshulkundaje/projects/blacklists)
46 contains useful information about regions with 60 contains useful information about regions with
47 unusually high counts."/> 61 unusually high counts."/>
48 62
49 <param name="outFileCorMatrix" type="boolean" label="Save the matrix of values underlying the heatmap"/> 63 <param name="outFileCorMatrix" type="boolean" label="Save the matrix of values underlying the heatmap"/>
50 <expand macro="heatmap_options" />
51 64
52 </inputs> 65 </inputs>
53 <outputs> 66 <outputs>
54 <expand macro="output_image_file_format" /> 67 <expand macro="output_image_file_format_not_nested" />
55 <data format="tabular" name="matrix" label="${tool.name} on ${on_string}: Correlation matrix"> 68 <data format="tabular" name="matrix" label="${tool.name} on ${on_string}: Correlation matrix">
56 <filter>outFileCorMatrix is True</filter> 69 <filter>outFileCorMatrix is True</filter>
57 </data> 70 </data>
58 </outputs> 71 </outputs>
59 <tests> 72 <tests>
68 <param name="corData" value="bamCorrelate_result1.npz" ftype="deeptools_coverage_matrix" /> 81 <param name="corData" value="bamCorrelate_result1.npz" ftype="deeptools_coverage_matrix" />
69 <param name="outFileFormat" value="png" /> 82 <param name="outFileFormat" value="png" />
70 <param name="whatToPlot" value="scatterplot" /> 83 <param name="whatToPlot" value="scatterplot" />
71 <param name="removeOutliers" value="True" /> 84 <param name="removeOutliers" value="True" />
72 <param name="plotTitle" value="Test Plot" /> 85 <param name="plotTitle" value="Test Plot" />
73 <output name="outFileName" file="plotCorrelation_result2.png" compare="sim_size" delta="100" /> 86 <output name="outFileName" file="plotCorrelation_result2.png" ftpye="png" compare="sim_size" delta="100" />
74 </test> 87 </test>
75 </tests> 88 </tests>
76 <help> 89 <help>
77 <![CDATA[ 90 <![CDATA[
78 **What it does** 91 **What it does**