Mercurial > repos > bgruening > hicexplorer_hicplotaverageregions

comparison hicPlotAverageRegions.xml @ 6:5fb461d15c31 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
author iuc
date Tue, 16 Mar 2021 15:35:10 +0000
parents 0dff8b5011c0
children ea5d67ec94ab
comparison
equal deleted inserted replaced
5:8f4b98b0f9a9 6:5fb461d15c31
1 <tool id="hicexplorer_hicplotaverageregions" name="@BINARY@" version="@WRAPPER_VERSION@.0"> 1 <tool id="hicexplorer_hicplotaverageregions" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
2 <description>plot the average regions from hicAverageRegions</description> 2 <description>plot the average regions from hicAverageRegions</description>
3 <macros> 3 <macros>
4 <token name="@BINARY@">hicPlotAverageRegions</token> 4 <token name="@BINARY@">hicPlotAverageRegions</token>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
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
41 <param argument="--vMin" type="float" optional="true" label="vMin" help="Minimum value of the plotted score."/> 41 <param argument="--vMin" type="float" optional="true" label="vMin" help="Minimum value of the plotted score." />
42 <param argument="--vMax" type="float" optional="true" label="vMax" help="Maximum value of the plotted score."/> 42 <param argument="--vMax" type="float" optional="true" label="vMax" help="Maximum value of the plotted score." />
43 43
44 <param name="image_file_format" type="select" label="Image output format"> 44 <param name="image_file_format" type="select" label="Image output format">
45 <option value="png" selected="True">png</option> 45 <option value="png" selected="True">png</option>
46 <option value="svg">svg</option> 46 <option value="svg">svg</option>
47 <option value="pdf">pdf</option> 47 <option value="pdf">pdf</option>
48 </param> 48 </param>
49 <param name='dpi' type='integer' label='DPI for image' help='Change the default resolution of the plot.' optional='true'/> 49 <expand macro="dpi" />
50
51 </inputs> 50 </inputs>
52 <outputs> 51 <outputs>
53 <data format="png" name="outFileName" from_work_dir="plot" label="${tool.name} [${on_string}]: Plot"> 52 <data format="png" name="outFileName" from_work_dir="plot" label="${tool.name} [${on_string}]: Plot">
54 <change_format> 53 <change_format>
55 <when input="image_file_format" value="svg" format="svg" /> 54 <when input="image_file_format" value="svg" format="svg" />
56 <when input="image_file_format" value="pdf" format="pdf" /> 55 <when input="image_file_format" value="pdf" format="pdf" />
57 </change_format> 56 </change_format>
58 </data> 57 </data>
59
60 </outputs> 58 </outputs>
61 <tests> 59 <tests>
62 <test> 60 <test>
63 <param name="matrix" value="hicAverageRegions/result_range_100000.npz" ftype="zip"/> 61 <param name="matrix" value="hicAverageRegions/result_range_100000.npz" ftype="zip" />
64 <param name="colormap" value="RdYlBu_r"/> 62 <param name="colormap" value="RdYlBu_r" />
65 <param name='dpi' value='10' /> 63 <param name='dpi' value='10' />
66 <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" />
67 </test> 65 </test>
68 <test> 66 <test>
69 <param name="matrix" value="hicAverageRegions/result_range_100000.npz" ftype="zip"/> 67 <param name="matrix" value="hicAverageRegions/result_range_100000.npz" ftype="zip" />
70 <param name="colormap" value="RdYlBu_r"/> 68 <param name="colormap" value="RdYlBu_r" />
71 <param name="log" value="True"/> 69 <param name="log" value="True" />
72 <param name='dpi' value='10' /> 70 <param name='dpi' value='10' />
73 71 <output name="outFileName" file="hicPlotAverageRegions/defaults_log.png" ftype="png" compare="sim_size" />
74
75 <output name="outFileName" file="hicPlotAverageRegions/defaults_log.png" ftype="png" compare="sim_size"/>
76 </test> 72 </test>
77 <test> 73 <test>
78 <param name="matrix" value="hicAverageRegions/result_range_100000.npz" ftype="zip"/> 74 <param name="matrix" value="hicAverageRegions/result_range_100000.npz" ftype="zip" />
79 <param name="colormap" value="RdYlBu_r"/> 75 <param name="colormap" value="RdYlBu_r" />
80 <param name="log1p" value="True"/> 76 <param name="log1p" value="True" />
81 <param name='dpi' value='10' /> 77 <param name='dpi' value='10' />
82 78 <output name="outFileName" file="hicPlotAverageRegions/defaults_log1p.png" ftype="png" compare="sim_size" />
83
84 <output name="outFileName" file="hicPlotAverageRegions/defaults_log1p.png" ftype="png" compare="sim_size"/>
85 </test> 79 </test>
86 <test> 80 <test>
87 <param name="matrix" value="hicAverageRegions/result_range_100000.npz" ftype="zip"/> 81 <param name="matrix" value="hicAverageRegions/result_range_100000.npz" ftype="zip" />
88 <param name="colormap" value="plasma"/> 82 <param name="colormap" value="plasma" />
89 <param name="vMax" value="20"/> 83 <param name="vMax" value="20" />
90 <param name="vMin" value="10"/> 84 <param name="vMin" value="10" />
91 <param name='dpi' value='10' /> 85 <param name='dpi' value='10' />
92 86 <output name="outFileName" file="hicPlotAverageRegions/defaults_log_vmin_vmax.png" ftype="png" compare="sim_size" />
93 <output name="outFileName" file="hicPlotAverageRegions/defaults_log_vmin_vmax.png" ftype="png" compare="sim_size"/>
94 </test> 87 </test>
95 </tests> 88 </tests>
96 <help><![CDATA[ 89 <help><![CDATA[
90
97 Plot of hicAverageRegions matrix 91 Plot of hicAverageRegions matrix
98 ================================ 92 ================================
99 hicPlotAverage regions plots the data computed by hicAverageRegions. It shows the summed up and averaged regions around all given reference points. This is useful to determine the difference between samples if the TAD configuration is equal or changed. 93 hicPlotAverage regions plots the data computed by hicAverageRegions. It shows the summed up and averaged regions around all given reference points. This is useful to determine the difference between samples if the TAD configuration is equal or changed.
100 94
101 95
102 | For more information about HiCExplorer please consider our documentation on readthedocs.io_ 96 | For more information about HiCExplorer please consider our documentation on readthedocs.io_
103 97
104 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html 98 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
105 ]]></help> 99 ]]> </help>
106 <expand macro="citations" /> 100 <expand macro="citations" />
107 </tool> 101 </tool>