Mercurial > repos > bgruening > hicexplorer_hicplotviewpoint

annotate hicPlotViewpoint.xml @ 15:58de3c7c8e89 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
author iuc
date Wed, 18 Oct 2023 11:08:32 +0000
parents b637a1e3cb14
children 8d203e74869b
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1 <tool id="hicexplorer_hicplotviewpoint" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
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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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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" help="The format is chr:referencePoint or chr:regionStart-regionEnd.">
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36 <validator type="expression" message="Only alphanumeric characters, the colon or a dash are allowed.">not value or value.replace(':', '').replace('-', '').isalnum()</validator>
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37 </param>
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38 <param argument="--interactionOutFileName" type="boolean" truevalue="--interactionOutFileName" falsevalue="" checked="false" label="Create bedgraph file with interactions" />
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39 <param name="image_file_format" type="select" label="Image output format">
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40 <option value="png">png</option>
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41 <option value="svg">svg</option>
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42 </param>
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43 </inputs>
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44 <outputs>
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45 <data format="png" name="outFileName" from_work_dir="plot" label="${tool.name} [${on_string}]: Plot">
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46 <change_format>
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47 <when input="image_file_format" value="png" format="png" />
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48 <when input="image_file_format" value="svg" format="svg" />
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49 </change_format>
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50 </data>
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51 <data format="bedgraph" name="interactionFile">
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52 <filter>interactionOutFileName</filter>
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53 <discover_datasets pattern='__name_and_ext__' directory="interaction" visible="true" />
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54 </data>
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55 </outputs>
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56 <tests>
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57 <test expect_num_outputs="1">
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58 <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.cool" />
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59 <param name="image_file_format" value="png" />
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60 <param name="region" value="X:3000000-3500000" />
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61 <param name="referencePoint" value="X:3200000" />
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62 <output name="outFileName" file="li_viewpoint_32Mb.png" ftype="png" compare="sim_size" />
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63 </test>
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64 <test expect_num_outputs="2">
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65 <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.cool" />
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66 <param name="image_file_format" value="png" />
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67 <param name="region" value="X:3000000-3500000" />
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68 <param name="referencePoint" value="X:3200000-3300000" />
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69 <param name="interactionOutFileName" value="True" />
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70 <output name="outFileName" file="li_viewpoint_32-33Mb.png" ftype="png" compare="sim_size" />
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71 <output name="interactionFile">
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72 <discovered_dataset designation="0_interactions" file="li_32-33mb_interactions.bedgraph" />
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73 </output>
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74 </test>
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75 </tests>
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76 <help><![CDATA[
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77
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78 Plot Viewpoint
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79 ==============
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80
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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.
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82 This plotting method allows to make long-range interactions more visible.
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83
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84 _________________
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85
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86 Usage
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87 -----
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88
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89 This tool must be used on Hi-C contact matrices corrected using ``hicCorrectMatrix``.
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91 _________________
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93 Output
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94 ------
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95
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96 **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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97
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98 .. image:: $PATH_TO_IMAGES/pulication_plots_viewpoint.png
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99 :width: 50 %
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101 _________________
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103 | For more information about HiCExplorer please consider our documentation on readthedocs.io_
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104
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105 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
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106 ]]> </help>
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107 <expand macro="citations" />
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108 </tool>