Mercurial > repos > bgruening > hicexplorer_hicplotviewpoint

comparison hicPlotViewpoint.xml @ 16:d488967c1625 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 14:01:01 +0000
parents 4b4d91356d93
children a1e583dc6579
comparison
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15:9b4e701157a4 16:d488967c1625
1 <tool id="hicexplorer_hicplotviewpoint" name="@BINARY@" version="@WRAPPER_VERSION@.0"> 1 <tool id="hicexplorer_hicplotviewpoint" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
2 <description>plot interactions around a viewpoint</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>
30 ]]> 30 ]]>
31 </command> 31 </command>
32 <inputs> 32 <inputs>
33 <expand macro='matrix_h5_cooler_multiple_macro' /> 33 <expand macro='matrix_h5_cooler_multiple_macro' />
34 <expand macro="region" /> 34 <expand macro="region" />
35 <param name="referencePoint" type="text" label="Reference point" 35 <param name="referencePoint" type="text" label="Reference point" help="The format is chr:referencePoint or chr:regionStart-regionEnd.">
36 help="The format is chr:referencePoint or chr:regionStart-regionEnd."/> 36 <validator type="expression" message="Only alphanumeric characters, the colon or a dash are allowed.">not value or value.replace(':', '').replace('-', '').isalnum()</validator>
37 37 </param>
38 <param name="interactionOutFileName" type="boolean" truevalue="--interactionOutFileName" falsevalue="" checked="false" 38 <param argument="--interactionOutFileName" type="boolean" truevalue="--interactionOutFileName" falsevalue="" checked="false" label="Create bedgraph file with interactions" />
39 label="Create bedgraph file with interactions" />
40 <param name="image_file_format" type="select" label="Image output format"> 39 <param name="image_file_format" type="select" label="Image output format">
41 <option value="png">png</option> 40 <option value="png">png</option>
42 <option value="svg">svg</option> 41 <option value="svg">svg</option>
43 </param> 42 </param>
44
45 </inputs> 43 </inputs>
46 <outputs> 44 <outputs>
47
48 <data format="png" name="outFileName" from_work_dir="plot" label="${tool.name} [${on_string}]: Plot"> 45 <data format="png" name="outFileName" from_work_dir="plot" label="${tool.name} [${on_string}]: Plot">
49 <change_format> 46 <change_format>
50 <when input="image_file_format" value="png" format="png" /> 47 <when input="image_file_format" value="png" format="png" />
51 <when input="image_file_format" value="svg" format="svg" /> 48 <when input="image_file_format" value="svg" format="svg" />
52 </change_format> 49 </change_format>
53 </data> 50 </data>
54 51 <data format="bedgraph" name="interactionFile">
55 <data format="bedgraph" name="interactionFile" >
56 <filter>interactionOutFileName</filter> 52 <filter>interactionOutFileName</filter>
57 <discover_datasets pattern='__name_and_ext__' directory="interaction" visible="true"/> 53 <discover_datasets pattern='__name_and_ext__' directory="interaction" visible="true" />
58 </data> 54 </data>
59
60 </outputs> 55 </outputs>
61 <tests> 56 <tests>
62 <test> 57 <test>
63 <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.cool"/> 58 <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.cool" />
64 <param name="image_file_format" value="png" /> 59 <param name="image_file_format" value="png" />
65 <param name='region' value='X:3000000-3500000' /> 60 <param name='region' value='X:3000000-3500000' />
66 <param name='referencePoint' value='X:3200000' /> 61 <param name='referencePoint' value='X:3200000' />
67 <output name="outFileName" file="li_viewpoint_32Mb.png" ftype="png" compare="sim_size"/> 62 <output name="outFileName" file="li_viewpoint_32Mb.png" ftype="png" compare="sim_size" />
68 </test> 63 </test>
69 <test> 64 <test>
70 <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.cool"/> 65 <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.cool" />
71 <param name="image_file_format" value="png" /> 66 <param name="image_file_format" value="png" />
72 <param name='region' value='X:3000000-3500000' /> 67 <param name='region' value='X:3000000-3500000' />
73 <param name='referencePoint' value='X:3200000-3300000' /> 68 <param name='referencePoint' value='X:3200000-3300000' />
74 <param name='interactionOutFileName' value='True' /> 69 <param name='interactionOutFileName' value='True' />
75 <output name="outFileName" file="li_viewpoint_32-33Mb.png" ftype="png" compare="sim_size"/> 70 <output name="outFileName" file="li_viewpoint_32-33Mb.png" ftype="png" compare="sim_size" />
76 <output name="interactionFile"> 71 <output name="interactionFile">
77 <discovered_dataset designation="0_interactions" file="li_32-33mb_interactions.bedgraph" /> 72 <discovered_dataset designation="0_interactions" file="li_32-33mb_interactions.bedgraph" />
78 </output> 73 </output>
79 </test> 74 </test>
80 </tests> 75 </tests>
81 <help><![CDATA[ 76 <help><![CDATA[
77
82 Plot Viewpoint 78 Plot Viewpoint
83 ============== 79 ==============
84 80
85 **hicPlotViewpoint** plots the number of interactions around a specific reference point or region in the genome like a 4C analysis using Hi-C data. 81 **hicPlotViewpoint** plots the number of interactions around a specific reference point or region in the genome like a 4C analysis using Hi-C data.
86 This plotting method allows to make long-range interactions more visible. 82 This plotting method allows to make long-range interactions more visible.
105 _________________ 101 _________________
106 102
107 | For more information about HiCExplorer please consider our documentation on readthedocs.io_ 103 | For more information about HiCExplorer please consider our documentation on readthedocs.io_
108 104
109 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html 105 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
110 ]]></help> 106 ]]> </help>
111 <expand macro="citations" /> 107 <expand macro="citations" />
112 </tool> 108 </tool>