Mercurial > repos > bgruening > hicexplorer_hicplotsvl

annotate hicPlotSVL.xml @ 1:ec91f79c59bb draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
author bgruening
date Wed, 05 Feb 2020 20:03:49 -0500
parents 450605e43e25
children 3a7752b8d2cb
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1 <tool id="hicexplorer_hicplotsvl" name="@BINARY@" version="@WRAPPER_VERSION@.0">
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2 <description>plots the relation of short vs long range contacts</description>
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3 <macros>
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4 <token name="@BINARY@">hicPlotSVL</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 #import re
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11 #for $counter, $m in enumerate($matrix_h5_cooler_multiple):
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12 #set identifier = @ESCAPE_IDENTIFIER_M@
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13 ln -s '$m' '${counter}_$identifier' &&
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14 #end for
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15 #set $m = ' '.join([ '\'%s_%s\'' % ($counter, @ESCAPE_IDENTIFIER_MATRIX@) for $counter, $matrix in enumerate($matrix_h5_cooler_multiple) ])
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17 @BINARY@
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18 --matrices $m
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19 #if $distance:
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20 --distance $distance
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21 #end if
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23 @CHROMOSOME_LIST@
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25 #if $colorList:
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26 #set $colorList_new = ' '.join([ '\'%s\'' % $color for $color in str($colorList).split(' ') ])
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27 --colorList $colorList_new
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28 #end if
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29
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30 #if $dpi:
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31 --dpi $dpi
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32 #end if
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33 --plotFileName plot.$image_file_format
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34 --outFileName p_values.txt
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35 --outFileNameData ratios.txt
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36 --threads @THREADS@
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37
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38 && mv plot.$image_file_format plot
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39 ]]>
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40 </command>
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41 <inputs>
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42 <expand macro='matrix_h5_cooler_multiple_macro'/>
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43 <param argument="--distance" optional='true' type="integer" label="Short range distance"
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44 help="Distance which should be considered as short range. Default 2MB." value='2000000'/>
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45 <expand macro="chromosome_list" />
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46 <param argument="--colorList" optional='true' type="text" label="Colorlist" help="Colorlist for the boxplots." />
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47 <param name='dpi' type='integer' label='DPI for image' help='Change the default resolution of the plot.' optional='true'/>
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48 <param name="image_file_format" type="select" label="Image output format">
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49 <option value="png" selected="True">png</option>
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50 <option value="svg">svg</option>
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51 <option value="pdf">pdf</option>
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52 </param>
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53 </inputs>
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54 <outputs>
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55 <data name='output_plot' from_work_dir='plot' format='png' label='Plot SVL'>
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56 <change_format>
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57 <when input="image_file_format" value="svg" format="svg" />
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58 <when input="image_file_format" value="pdf" format="pdf" />
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59 </change_format>
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60 </data>
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61 <data name='output_p_values' from_work_dir='p_values.txt' format='txt' label='P values svl'/>
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62 <data name='output_ratios' from_work_dir='ratios.txt' format='txt' label='Ratios svl'/>
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63
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64 </outputs>
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65 <tests>
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66 <test>
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67 <param name="matrix_h5_cooler_multiple" value="small_test_matrix.h5,small_test_matrix.h5"/>
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68 <param name="distance" value="2000000"/>
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69 <param name="dpi" value="10"/>
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70 <param name="color" value="y m c"/>
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71 <repeat name="chromosome_list">
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72 <param name="chromosomes" value="chr2L"/>
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73 </repeat>
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74 <repeat name="chromosome_list">
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75 <param name="chromosomes" value="chr3L"/>
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76 </repeat>
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77 <repeat name="chromosome_list">
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78 <param name="chromosomes" value="chr4"/>
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79 </repeat>
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80
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81 <param name="image_file_format" value="png" />
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82
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83 <output name="output_plot" file="hicPlotSVL/plot.png" ftype="png" compare="sim_size"/>
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84 <output name="output_p_values" file="hicPlotSVL/p_values.txt" ftype="txt" compare="sim_size"/>
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85 <output name="output_ratios" file="hicPlotSVL/ratios.txt" ftype="txt" compare="sim_size"/>
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86
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87 </test>
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88 </tests>
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89 <help><![CDATA[
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90
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91 Short vs long range contacts
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92 ============================
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93
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94 Computes the ratio of short vs. long range contacts on the given matrices and makes, if two or more matrices are present a differential test between the matrices.
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95
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96 For more information about HiCExplorer please consider our documentation on readthedocs.io_.
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97
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98 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
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99
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100 ]]></help>
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101 <expand macro="citations" />
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102 </tool>