Mercurial > repos > bgruening > hicexplorer_hicplotaverageregions

comparison hicPlotAverageRegions.xml @ 8:ea5d67ec94ab draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
author iuc
date Wed, 18 Oct 2023 10:35:07 +0000
parents 5fb461d15c31
children
comparison
equal deleted inserted replaced
7:f490a6409f3d 8:ea5d67ec94ab
30 30
31 && mv plot.$image_file_format plot 31 && mv plot.$image_file_format plot
32 ]]> 32 ]]>
33 </command> 33 </command>
34 <inputs> 34 <inputs>
35 <param argument="--matrix" type="data" format='zip' label="Average regions matrix computed by hicAverageRegions" /> 35 <param argument="--matrix" type="data" format="zip" label="Average regions matrix computed by hicAverageRegions" />
36 <param argument="--log1p" type="boolean" truevalue="--log1p" falsevalue="" checked="false" label="Plot the log1p of the matrix values (log(Hi-C contacts+1)). This option is recommended." /> 36 <param argument="--log1p" type="boolean" truevalue="--log1p" falsevalue="" checked="false" label="Plot the log1p of the matrix values (log(Hi-C contacts+1)). This option is recommended." />
37 <param argument="--log" type="boolean" truevalue="--log" falsevalue="" checked="false" label="Plot the log of the matrix values. (log(Hi-C contacts))" /> 37 <param argument="--log" type="boolean" truevalue="--log" falsevalue="" checked="false" label="Plot the log of the matrix values. (log(Hi-C contacts))" />
38 38
39 <expand macro="colormap" /> 39 <expand macro="colormap" />
40 40
58 </outputs> 58 </outputs>
59 <tests> 59 <tests>
60 <test> 60 <test>
61 <param name="matrix" value="hicAverageRegions/result_range_100000.npz" ftype="zip" /> 61 <param name="matrix" value="hicAverageRegions/result_range_100000.npz" ftype="zip" />
62 <param name="colormap" value="RdYlBu_r" /> 62 <param name="colormap" value="RdYlBu_r" />
63 <param name='dpi' value='10' /> 63 <param name="dpi" value="10" />
64 <output name="outFileName" file="hicPlotAverageRegions/defaults.png" ftype="png" compare="sim_size" /> 64 <output name="outFileName" file="hicPlotAverageRegions/defaults.png" ftype="png" compare="sim_size" />
65 </test> 65 </test>
66 <test> 66 <test>
67 <param name="matrix" value="hicAverageRegions/result_range_100000.npz" ftype="zip" /> 67 <param name="matrix" value="hicAverageRegions/result_range_100000.npz" ftype="zip" />
68 <param name="colormap" value="RdYlBu_r" /> 68 <param name="colormap" value="RdYlBu_r" />
69 <param name="log" value="True" /> 69 <param name="log" value="True" />
70 <param name='dpi' value='10' /> 70 <param name="dpi" value="10" />
71 <output name="outFileName" file="hicPlotAverageRegions/defaults_log.png" ftype="png" compare="sim_size" /> 71 <output name="outFileName" file="hicPlotAverageRegions/defaults_log.png" ftype="png" compare="sim_size" />
72 </test> 72 </test>
73 <test> 73 <test>
74 <param name="matrix" value="hicAverageRegions/result_range_100000.npz" ftype="zip" /> 74 <param name="matrix" value="hicAverageRegions/result_range_100000.npz" ftype="zip" />
75 <param name="colormap" value="RdYlBu_r" /> 75 <param name="colormap" value="RdYlBu_r" />
76 <param name="log1p" value="True" /> 76 <param name="log1p" value="True" />
77 <param name='dpi' value='10' /> 77 <param name="dpi" value="10" />
78 <output name="outFileName" file="hicPlotAverageRegions/defaults_log1p.png" ftype="png" compare="sim_size" /> 78 <output name="outFileName" file="hicPlotAverageRegions/defaults_log1p.png" ftype="png" compare="sim_size" />
79 </test> 79 </test>
80 <test> 80 <test>
81 <param name="matrix" value="hicAverageRegions/result_range_100000.npz" ftype="zip" /> 81 <param name="matrix" value="hicAverageRegions/result_range_100000.npz" ftype="zip" />
82 <param name="colormap" value="plasma" /> 82 <param name="colormap" value="plasma" />
83 <param name="vMax" value="20" /> 83 <param name="vMax" value="20" />
84 <param name="vMin" value="10" /> 84 <param name="vMin" value="10" />
85 <param name='dpi' value='10' /> 85 <param name="dpi" value="10" />
86 <output name="outFileName" file="hicPlotAverageRegions/defaults_log_vmin_vmax.png" ftype="png" compare="sim_size" /> 86 <output name="outFileName" file="hicPlotAverageRegions/defaults_log_vmin_vmax.png" ftype="png" compare="sim_size" />
87 </test> 87 </test>
88 </tests> 88 </tests>
89 <help><![CDATA[ 89 <help><![CDATA[
90 90