Mercurial > repos > bgruening > hicexplorer_hicplotviewpoint

annotate hicPlotViewpoint.xml @ 7:5e9c304c424c draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
author bgruening
date Mon, 16 Dec 2019 15:42:31 -0500
parents 67bd57e960a3
children 84d4b83f092a
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58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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1 <tool id="hicexplorer_hicplotviewpoint" name="@BINARY@" version="@WRAPPER_VERSION@.0">
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2 <description>plot interactions around a viewpoint</description>
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3 <macros>
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4 <token name="@BINARY@">hicPlotViewpoint</token>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="requirements" />
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8 <command detect_errors="exit_code"><![CDATA[
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9
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10 #for $counter, $m in enumerate($matrix_h5_cooler_multiple):
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11 ln -s '$m' ${counter}_matrix.$m.ext &&
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12 #end for
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13 #set $m = ' '.join([ '\'%s_matrix.%s\'' % ($counter, $matrix.ext) for $counter, $matrix in enumerate($matrix_h5_cooler_multiple) ])
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15 @BINARY@ --matrix $m
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16 #if $interactionOutFileName:
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17 $interactionOutFileName interactions
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18 #end if
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19 --outFileName plot.$image_file_format
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20 --region $region
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21 --referencePoint $referencePoint
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22 && mv plot.$image_file_format plot
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23
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24 #if $interactionOutFileName:
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25 && mkdir interaction
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26 #for $counter, $matrix in enumerate($m.split(' ')):
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27 && mv interactions_${matrix}.bedgraph interaction/${counter}_interactions.bedgraph
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28 #end for
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29 #end if
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30 ]]>
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31 </command>
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32 <inputs>
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33 <expand macro='matrix_h5_cooler_multiple_macro' />
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34 <expand macro="region" />
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35 <param name="referencePoint" type="text" label="Reference point"
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36 help="The format is chr:referencePoint or chr:regionStart-regionEnd."/>
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37
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38 <param name="interactionOutFileName" type="boolean" truevalue="--interactionOutFileName" falsevalue="" checked="false"
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39 label="Create bedgraph file with interactions" />
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40 <param name="image_file_format" type="select" label="Image output format">
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41 <option value="png">png</option>
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42 <option value="svg">svg</option>
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43 </param>
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45 </inputs>
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46 <outputs>
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47
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48 <data format="png" name="outFileName" from_work_dir="plot" label="${tool.name} [${on_string}]: Plot">
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49 <change_format>
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50 <when input="image_file_format" value="png" format="png" />
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51 <when input="image_file_format" value="svg" format="svg" />
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52 </change_format>
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53 </data>
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55 <data format="bedgraph" name="interactionFile" >
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56 <filter>interactionOutFileName</filter>
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57 <discover_datasets pattern='__name_and_ext__' directory="interaction" visible="true"/>
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58 </data>
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59
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60 </outputs>
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61 <tests>
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62 <test>
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63 <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.cool"/>
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64 <param name="image_file_format" value="png" />
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65 <param name='region' value='X:3000000-3500000' />
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66 <param name='referencePoint' value='X:3200000' />
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67 <output name="outFileName" file="li_viewpoint_32Mb.png" ftype="png" compare="sim_size"/>
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68 </test>
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69 <test>
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70 <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.cool"/>
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71 <param name="image_file_format" value="png" />
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72 <param name='region' value='X:3000000-3500000' />
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73 <param name='referencePoint' value='X:3200000-3300000' />
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74 <param name='interactionOutFileName' value='True' />
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75 <output name="outFileName" file="li_viewpoint_32-33Mb.png" ftype="png" compare="sim_size"/>
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76 <output name="interactionFile">
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77 <discovered_dataset designation="0_interactions" file="li_32-33mb_interactions.bedgraph" />
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78 </output>
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79 </test>
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80 </tests>
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81 <help><![CDATA[
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82 Plot Viewpoint
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83 ==============
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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.
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86 This plotting method allows to make long-range interactions more visible.
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88 _________________
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90 Usage
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91 -----
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92
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93 This tool must be used on Hi-C contact matrices corrected using ``hicCorrectMatrix``.
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95 _________________
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97 Output
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98 ------
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100 **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.
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102 .. image:: $PATH_TO_IMAGES/pulication_plots_viewpoint.png
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103 :width: 50 %
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105 _________________
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107 | For more information about HiCExplorer please consider our documentation on readthedocs.io_
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109 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
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110 ]]></help>
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111 <expand macro="citations" />
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112 </tool>