Mercurial > repos > bgruening > hicexplorer_hicplotmatrix
annotate hicPlotMatrix.xml @ 4:fd5e51d2b558 draft
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
author | iuc |
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date | Sat, 16 Dec 2017 16:30:53 -0500 |
parents | 2c0069f645bc |
children | c3703afea1b1 |
rev | line source |
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4
fd5e51d2b558
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
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1 <tool id="hicexplorer_hicplotmatrix" name="@BINARY@" version="@WRAPPER_VERSION@.1"> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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2 <description>Plots a HiC matrix heatmap</description> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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3 <macros> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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4 <token name="@BINARY@">hicPlotMatrix</token> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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5 <import>macros.xml</import> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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6 </macros> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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7 <expand macro="requirements" /> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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8 <command detect_errors="exit_code"><![CDATA[ |
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9 ln -s '$matrix' input_matrix.h5 && |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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10 |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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11 @BINARY@ |
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12 |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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13 --matrix input_matrix.h5 |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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14 |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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15 #if $title and $title is not None: |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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16 --title '$title' |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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17 #end if |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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18 |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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19 #if $scoreName and $scoreName is not None: |
a9050bffb50c
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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20 --scoreName '$scoreName' |
a9050bffb50c
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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21 #end if |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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22 |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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23 |
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2c0069f645bc
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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24 --outFileName plot.$image_file_format |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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25 |
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26 $perChromosome |
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27 $clearMaskedBins |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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28 |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
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29 --whatToShow heatmap |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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30 |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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31 |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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32 ## special: --chromosomeOrder is optional, but if given needs at least one argument |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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33 #set chroms = '" "'.join([ str($var.chromosome) for $var in $chromosomeOrder ]) |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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34 #if chroms: |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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35 --chromosomeOrder '$chroms' |
a9050bffb50c
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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36 #end if |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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37 |
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38 #if $region: |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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39 --region '$region' |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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40 #end if |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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41 |
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42 #if $region2: |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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43 --region2 '$region2' |
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44 #end if |
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45 $log1p |
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46 $log |
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47 |
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48 #if $colormap: |
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49 --colorMap $colormap |
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50 #end if |
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51 |
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52 #if $vMin: |
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53 --vMin $vMin |
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54 #end if |
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55 |
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56 #if $vMax: |
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57 --vMax $vMax |
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58 #end if |
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59 |
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60 && mv plot.$image_file_format plot |
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61 ]]> |
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62 </command> |
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63 <inputs> |
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64 <param argument="--matrix" type="data" format="h5" label="Hi-C matrix to plot"/> |
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65 <param argument="--title" type="text" optional="true" label="Plot title"/> |
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66 <param argument="--scoreName" type="text" optional="true" label="Score name"/> |
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67 <param argument="--perChromosome" type="boolean" truevalue="--perChromosome" falsevalue="" checked="false" |
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68 label="Plot per chromosome" |
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69 help="Instead of plotting the whole matrix each chromosome is plotted next to the other. This parameter is not compatible with --region" /> |
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70 <param argument="--clearMaskedBins" type="boolean" truevalue="--clearMaskedBins" falsevalue="" checked="false" |
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71 label="Remove masked bins from the matrix" /> |
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72 |
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73 <repeat name="chromosomeOrder" min="0" title="Chromosomes to include (and order to plot in):" |
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74 help="This option overrides --region and --region2" > |
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75 <param name="chromosome" type="text" > |
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76 <validator type="empty_field" /> |
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77 </param> |
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78 </repeat> |
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79 |
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80 <param argument="--region" type="text" optional="True" label="Plot only this region" |
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81 help="The format is chr:start-end The plotted region contains the main diagonal and is symmetric unless --region2 is given"/> |
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82 <param argument="--region2" type="text" optional="True" label="Region two to plot" |
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83 help="If given then only the region defined by --region and --region2 is plotted. The format is the same as --region"/> |
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84 <param argument="--log1p" type="boolean" truevalue="--log1p" falsevalue="" checked="false" label="Plot the log1p of the matrix values."/> |
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85 <param argument="--log" type="boolean" truevalue="--log" falsevalue="" checked="false" label="Plot the log of the matrix values."/> |
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86 |
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87 <expand macro="colormap" /> |
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88 |
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89 <param argument="--vMin" type="float" optional="true" label="vMin"/> |
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90 <param argument="--vMax" type="float" optional="true" label="vMax"/> |
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91 <param name="image_file_format" type="select" label="Image output format"> |
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92 <option value="png" selected="True">png</option> |
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93 <option value="svg">svg</option> |
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94 </param> |
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95 </inputs> |
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96 <outputs> |
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97 <data format="png" name="outFileName" from_work_dir="plot" label="${tool.name} on ${on_string}"> |
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98 <change_format> |
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99 <when input="image_file_format" value="svg" format="svg" /> |
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100 </change_format> |
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101 </data> |
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102 </outputs> |
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103 <tests> |
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104 <test> |
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105 <param name="matrix" ftype="h5" value="Li_et_al_2015.h5"/> |
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106 <param name="region" value="chrX:3000000-3500000"/> |
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107 <param name="region2" value="chrX:3100000-3600000"/> |
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108 <param name="log1p" value="True"/> |
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109 <param name="clearMaskedBins" value="True"/> |
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110 <!-- <param name="whatToShow_select" value="heatmap"/> --> |
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111 <param name="image_file_format" value="png" /> |
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112 <output name="outFileName" file="master_matrix_plot.png" ftype="png" compare="sim_size"/> |
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113 </test> |
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114 </tests> |
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115 <help><![CDATA[ |
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116 Contact matrix plot |
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117 ======================= |
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118 |
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119 ``hicPlotMatrix`` is a visualization tool for a contact matrix. It supports to plot the whole contact matrix, one or more chromosomes, a region or two regions against each other. |
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120 |
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121 .. Additional it can plot the result of a principal component analysis to have a better understanding of A / B compartments. |
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122 |
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123 Input |
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124 ----- |
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125 |
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126 Parameters |
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127 __________ |
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128 - the contact matrix |
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129 - A title for the plot |
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130 - Score name |
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131 - per chromosome |
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132 - The chromosomes to include in the plot. |
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133 - What to show: |
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134 - The region(s) to plot. This parameter overrides 'chromosome'. If either 'chromosomes' or 'region' is given the full contact matrix is used. |
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135 - log / log1p of the values: It is recommended to use log1p. |
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136 - Colormaps_ for the heatmap. |
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137 - vMin / vMax |
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138 |
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139 .. - principal component: a bedgraph file |
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140 |
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141 Output |
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142 ------ |
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143 |
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144 The contact matrix plotted for chromosome 1. |
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145 |
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146 .. image:: SRR027956.svg |
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147 :width: 70% |
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148 |
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149 |
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150 The contact matrix used with ``--perChr`` and the first eigenvector from the tool ``hicPCA``. For this plot a pearson correlated matrix was used which is computed by creating first an observed / expected matrix and second a pearson correlation matrix. These matricies can be computed with ``hicChangeMatrixType``. The used Hi-C data were published by `Lieberman-Aiden <https://doi.org/10.1126/science.1181369>`_ in 2009, `GSE18199 <https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18199>`_. |
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151 |
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152 .. image:: $PATH_TO_IMAGES/SRR0279XX_perChr_eigenvector1.png |
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153 :width: 70 % |
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154 |
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155 | For more information about HiCExplorer please consider our documentation on readthedocs.io_ |
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156 |
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157 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html |
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158 .. _Colormaps: https://matplotlib.org/examples/color/colormaps_reference.html |
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159 ]]></help> |
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160 <expand macro="citations" /> |
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161 </tool> |
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