Mercurial > repos > bgruening > hicexplorer_hicplotviewpoint

comparison hicPlotViewpoint.xml @ 3:745e77f4e81e draft

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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
author iuc
date Fri, 27 Apr 2018 03:35:16 -0400
parents 58d146c74d72
children c4f273c3c73f
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2:bb82a2982d3d 3:745e77f4e81e
1 <tool id="hicexplorer_hicplotviewpoint" name="@BINARY@" version="@WRAPPER_VERSION@.0"> 1 <tool id="hicexplorer_hicplotviewpoint" name="@BINARY@" version="@WRAPPER_VERSION@.0">
2 <description>computes the principal components for A / B compartment analysis</description> 2 <description>plot interactions around a viewpoint</description>
3 <macros> 3 <macros>
4 <token name="@BINARY@">hicPlotViewpoint</token> 4 <token name="@BINARY@">hicPlotViewpoint</token>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
7 <expand macro="requirements" /> 7 <expand macro="requirements" />
20 <inputs> 20 <inputs>
21 <expand macro='matrix_h5_cooler_macro' /> 21 <expand macro='matrix_h5_cooler_macro' />
22 <expand macro="region" /> 22 <expand macro="region" />
23 <param name="referencePoint" type="text" label="Reference point" 23 <param name="referencePoint" type="text" label="Reference point"
24 help="The format is chr:referencePoint or chr:regionStart-regionEnd."/> 24 help="The format is chr:referencePoint or chr:regionStart-regionEnd."/>
25 25
26 <param name="interactionOutFileName" type="boolean" truevalue="--interactionOutFileName" falsevalue="" checked="false" 26 <param name="interactionOutFileName" type="boolean" truevalue="--interactionOutFileName" falsevalue="" checked="false"
27 label="Create bedgraph file with interactions" /> 27 label="Create bedgraph file with interactions" />
28 <param name="image_file_format" type="select" label="Image output format"> 28 <param name="image_file_format" type="select" label="Image output format">
29 <option value="png">png</option> 29 <option value="png">png</option>
30 <option value="svg">svg</option> 30 <option value="svg">svg</option>
31 </param> 31 </param>
32 32
33 </inputs> 33 </inputs>
34 <outputs> 34 <outputs>
35 35
36 <data format="png" name="outFileName" from_work_dir="plot"> 36 <data format="png" name="outFileName" from_work_dir="plot" label="${tool.name} on ${matrix_h5_cooler.name} [${on_string}]: Plot">
37 <change_format> 37 <change_format>
38 <when input="image_file_format" value="png" format="png" /> 38 <when input="image_file_format" value="png" format="png" />
39 <when input="image_file_format" value="svg" format="svg" /> 39 <when input="image_file_format" value="svg" format="svg" />
40 </change_format> 40 </change_format>
41 </data> 41 </data>
42 <data name='interactionFile' from_work_dir='interactions.bedgraph' format='bedgraph'> 42 <data name='interactionFile' from_work_dir='interactions.bedgraph' format='bedgraph' label="${tool.name} on ${matrix_h5_cooler.name} [${on_string}]: Bedgraph">
43 <filter>interactionOutFileName</filter> 43 <filter>interactionOutFileName</filter>
44 </data> 44 </data>
45 45
46 </outputs> 46 </outputs>
47 <tests> 47 <tests>
48 <test> 48 <test>
49 <param name="matrix_h5_cooler" value="Li_et_al_2015.h5"/> 49 <param name="matrix_h5_cooler" value="Li_et_al_2015.h5"/>
50 <param name="image_file_format" value="png" /> 50 <param name="image_file_format" value="png" />
58 <param name='region' value='X:3000000-3500000' /> 58 <param name='region' value='X:3000000-3500000' />
59 <param name='referencePoint' value='X:3200000-3300000' /> 59 <param name='referencePoint' value='X:3200000-3300000' />
60 <param name='interactionOutFileName' value='True' /> 60 <param name='interactionOutFileName' value='True' />
61 <output name="outFileName" file="li_viewpoint_32-33Mb.png" ftype="png" compare="sim_size"/> 61 <output name="outFileName" file="li_viewpoint_32-33Mb.png" ftype="png" compare="sim_size"/>
62 <output name="interactionFile" file="li_32-33mb_interactions.bedgraph" ftype="bedgraph" compare="sim_size"/> 62 <output name="interactionFile" file="li_32-33mb_interactions.bedgraph" ftype="bedgraph" compare="sim_size"/>
63 63
64 </test> 64 </test>
65 </tests> 65 </tests>
66 <help><![CDATA[ 66 <help><![CDATA[
67 Principal component analysis 67 Plot Viewpoint
68 ============================ 68 ==============
69 `hicPCA` computes two eigenvector files based on the input matrix for an A / B compartment analysis.
70 69
71 Input 70 **hicPlotViewpoint** plots the number of interactions around a specific reference point or region in the genome like a 4C analysis using Hi-C data.
71 This plotting method allows to make long-range interactions more visible.
72
73 _________________
74
75 Usage
72 ----- 76 -----
73 - the matrix to be analysed
74 77
75 Parameters 78 This tool must be used on Hi-C contact matrices corrected using ``hicCorrectMatrix``.
76 __________ 79
77 - Output file format: bigwig or bedgraph 80 _________________
78 81
79 Output 82 Output
80 ------ 83 ------
81 Two files with the first and the second eigenvector. 84
85 **hicPlotViewpoint** outputs an image with the plotted interactions around the reference point in png or svg format, an example plot can be found bellow. An option allows to also output the interactions as a bedgraph file.
86
87 .. image:: $PATH_TO_IMAGES/pulication_plots_viewpoint.png
88 :width: 80 %
89
90 _________________
82 91
83 | For more information about HiCExplorer please consider our documentation on readthedocs.io_ 92 | For more information about HiCExplorer please consider our documentation on readthedocs.io_
84 93
85 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html 94 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
86 ]]></help> 95 ]]></help>