Mercurial > repos > bgruening > hicexplorer_hicplotviewpoint

annotate hicPlotViewpoint.xml @ 12:4b4d91356d93 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
author iuc
date Tue, 10 Mar 2020 19:11:34 +0000
parents e8a131f0840f
children d488967c1625
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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>
62d7796789e9 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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5 <import>macros.xml</import>
62d7796789e9 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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6 </macros>
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7 <expand macro="requirements" />
62d7796789e9 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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8 <command detect_errors="exit_code"><![CDATA[
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9
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e8a131f0840f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
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10 #for $counter, $m in enumerate($matrix_h5_cooler_multiple):
e8a131f0840f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
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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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4b4d91356d93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
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14
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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
62d7796789e9 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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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"
62d7796789e9 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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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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44
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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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54
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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
0
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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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84
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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>