Mercurial > repos > bgruening > hicexplorer_hicplotviewpoint

annotate hicPlotViewpoint.xml @ 3:63cc8b3c66da 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 03:11:44 -0400
parents 62d7796789e9
children d8cb9c850ebe
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62d7796789e9 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 hicPlotViewpoint --matrix '$matrix_h5_cooler'
62d7796789e9 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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11 #if $interactionOutFileName:
62d7796789e9 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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12 $interactionOutFileName interactions.bedgraph
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13 #end if
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14 --outFileName plot.$image_file_format
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15 --region $region
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16 --referencePoint $referencePoint
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17 && mv plot.$image_file_format plot
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18 ]]>
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19 </command>
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20 <inputs>
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21 <expand macro='matrix_h5_cooler_macro' />
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22 <expand macro="region" />
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23 <param name="referencePoint" type="text" label="Reference point"
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24 help="The format is chr:referencePoint or chr:regionStart-regionEnd."/>
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25
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26 <param name="interactionOutFileName" type="boolean" truevalue="--interactionOutFileName" falsevalue="" checked="false"
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27 label="Create bedgraph file with interactions" />
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28 <param name="image_file_format" type="select" label="Image output format">
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29 <option value="png">png</option>
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30 <option value="svg">svg</option>
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31 </param>
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32
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33 </inputs>
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34 <outputs>
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36 <data format="png" name="outFileName" from_work_dir="plot" label="${tool.name} on ${matrix_h5_cooler.name} [${on_string}]: Plot">
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37 <change_format>
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38 <when input="image_file_format" value="png" format="png" />
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39 <when input="image_file_format" value="svg" format="svg" />
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40 </change_format>
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41 </data>
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42 <data name='interactionFile' from_work_dir='interactions.bedgraph' format='bedgraph' label="${tool.name} on ${matrix_h5_cooler.name} [${on_string}]: Bedgraph">
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43 <filter>interactionOutFileName</filter>
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44 </data>
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45
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46 </outputs>
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47 <tests>
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48 <test>
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49 <param name="matrix_h5_cooler" value="Li_et_al_2015.h5"/>
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50 <param name="image_file_format" value="png" />
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51 <param name='region' value='X:3000000-3500000' />
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52 <param name='referencePoint' value='X:3200000' />
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53 <output name="outFileName" file="li_viewpoint_32Mb.png" ftype="png" compare="sim_size"/>
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54 </test>
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55 <test>
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56 <param name="matrix_h5_cooler" value="Li_et_al_2015.h5"/>
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57 <param name="image_file_format" value="png" />
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58 <param name='region' value='X:3000000-3500000' />
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59 <param name='referencePoint' value='X:3200000-3300000' />
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60 <param name='interactionOutFileName' value='True' />
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61 <output name="outFileName" file="li_viewpoint_32-33Mb.png" ftype="png" compare="sim_size"/>
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62 <output name="interactionFile" file="li_32-33mb_interactions.bedgraph" ftype="bedgraph" compare="sim_size"/>
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63
0
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64 </test>
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65 </tests>
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66 <help><![CDATA[
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67 Plot Viewpoint
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68 ==============
0
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69
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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.
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71 This plotting method allows to make long-range interactions more visible.
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73 _________________
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75 Usage
0
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76 -----
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77
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78 This tool must be used on Hi-C contact matrices corrected using ``hicCorrectMatrix``.
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80 _________________
0
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82 Output
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83 ------
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84
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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.
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87 .. image:: $PATH_TO_IMAGES/pulication_plots_viewpoint.png
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88 :width: 80 %
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90 _________________
0
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92 | For more information about HiCExplorer please consider our documentation on readthedocs.io_
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94 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
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95 ]]></help>
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96 <expand macro="citations" />
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97 </tool>