Mercurial > repos > bgruening > deeptools_plot_correlation
comparison plotCorrelation.xml @ 17:90d5df0a49bd draft
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
author | bgruening |
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date | Thu, 15 Feb 2018 05:49:05 -0500 |
parents | d40bd147adf3 |
children | 4e8b35fd2173 |
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16:a165d1e95d7d | 17:90d5df0a49bd |
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16 @HEATMAP_OPTIONS@ | 16 @HEATMAP_OPTIONS@ |
17 --plotWidth $plotting_type.plotWidth | 17 --plotWidth $plotting_type.plotWidth |
18 --plotHeight $plotting_type.plotHeight | 18 --plotHeight $plotting_type.plotHeight |
19 #else: | 19 #else: |
20 --plotTitle '$plotting_type.plotTitle' | 20 --plotTitle '$plotting_type.plotTitle' |
21 #if str($plotting_type.maxRange) != '': | |
22 --maxRange '$plotting_type.maxRange' | |
23 #end if | |
24 $plotting_type.log1p | |
21 #end if | 25 #end if |
22 $skipZeros | 26 $skipZeros |
23 --plotFileFormat "$outFileFormat" | 27 --plotFileFormat "$outFileFormat" |
24 $removeOutliers | 28 $removeOutliers |
25 #if $outFileCorMatrix: | 29 #if $outFileCorMatrix: |
41 <expand macro="heatmap_options" /> | 45 <expand macro="heatmap_options" /> |
42 <expand macro="plotWidthHeight" PLOTWIDTH="11.0" PLOTHEIGHT="9.5" /> | 46 <expand macro="plotWidthHeight" PLOTWIDTH="11.0" PLOTHEIGHT="9.5" /> |
43 </when> | 47 </when> |
44 <when value="scatterplot"> | 48 <when value="scatterplot"> |
45 <expand macro="plotTitle" /> | 49 <expand macro="plotTitle" /> |
50 <param argument="--maxRange" type="integer" value="" optional="true" | |
51 label="Maximum Range" | |
52 help="Maximum (integer) value for the X and Y axes. The default scales these such that the full range of dots is displayed. If you specify --log1p, please ensure that this value is within the range it will produce." /> | |
53 <param argument="--log1p" type="boolean" truevalue="--log1p" falsevalue="" | |
54 label="Log transform" | |
55 help="Plot the natural log of the scatter plot after adding 1. Note that this is ONLY for plotting, the correlation is unaffected." /> | |
46 </when> | 56 </when> |
47 </conditional> | 57 </conditional> |
48 | 58 |
49 <expand macro="skipZeros" /> | 59 <expand macro="skipZeros" /> |
50 | 60 |
76 <test> | 86 <test> |
77 <param name="corData" value="multiBamSummary_result1.npz" ftype="deeptools_coverage_matrix" /> | 87 <param name="corData" value="multiBamSummary_result1.npz" ftype="deeptools_coverage_matrix" /> |
78 <param name="outFileFormat" value="png" /> | 88 <param name="outFileFormat" value="png" /> |
79 <param name="outFileCorMatrix" value="True" /> | 89 <param name="outFileCorMatrix" value="True" /> |
80 <output name="matrix" file="plotCorrelation_result1.tabular" ftype="tabular" /> | 90 <output name="matrix" file="plotCorrelation_result1.tabular" ftype="tabular" /> |
81 <output name="outFileName" file="plotCorrelation_result1.png" ftype="png" compare="sim_size" delta="300" /> | 91 <output name="outFileName" file="plotCorrelation_result1.png" ftype="png" compare="sim_size" delta="400" /> |
82 </test> | 92 </test> |
83 <test> | 93 <test> |
84 <param name="corData" value="multiBamSummary_result1.npz" ftype="deeptools_coverage_matrix" /> | 94 <param name="corData" value="multiBamSummary_result1.npz" ftype="deeptools_coverage_matrix" /> |
85 <param name="outFileFormat" value="png" /> | 95 <param name="outFileFormat" value="png" /> |
86 <param name="whatToPlot" value="scatterplot" /> | 96 <param name="whatToPlot" value="scatterplot" /> |