Mercurial > repos > bgruening > hicexplorer_hiccompartmentspolarization

annotate hicCompartmentalization.xml @ 1:c6f32406aa3c 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 19:49:53 -0500
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children ed3dea19c464
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c6f32406aa3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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1 <tool id="hicexplorer_hiccompartmentspolarization" name="@BINARY@" version="@WRAPPER_VERSION@.0">
c6f32406aa3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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2 <description>compute pairwise correlations between multiple Hi-C contact matrices</description>
c6f32406aa3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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3 <macros>
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4 <token name="@BINARY@">hicCompartmentalization</token>
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5 <import>macros.xml</import>
c6f32406aa3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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6 </macros>
c6f32406aa3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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7 <expand macro="requirements" />
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8 <command detect_errors="exit_code"><![CDATA[
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9
c6f32406aa3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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10 #for $counter, $m in enumerate($matrix_h5_cooler_multiple):
c6f32406aa3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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11 ln -s '$m' '${counter}_matrix.$m.ext' &&
c6f32406aa3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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12 #end for
c6f32406aa3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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13 #set $m = ' '.join([ '\'%s_matrix.%s\'' % ($counter, $matrix.ext) for $counter, $matrix in enumerate($matrix_h5_cooler_multiple) ])
c6f32406aa3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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14
c6f32406aa3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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15 @BINARY@
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16
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17 --obsexp_matrices $m
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18
c6f32406aa3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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19 --pca '$pca'
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20 --quantile $quantile
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21
c6f32406aa3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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22 #if $set_offset_value:
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23 #set $offset_array = $set_offset_value.split(' ')
c6f32406aa3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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24 #set $offset = ' '.join([ '%s' % int($value) for $value in $offset_array ])
c6f32406aa3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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25 --offset $offset
c6f32406aa3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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26 #end if
c6f32406aa3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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27 --outliers $outliers
c6f32406aa3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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28 --outputFileName plot.$image_file_format
c6f32406aa3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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29
c6f32406aa3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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30 && mv plot.$image_file_format plot
c6f32406aa3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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31 ]]>
c6f32406aa3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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32 </command>
c6f32406aa3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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33 <inputs>
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34 <expand macro="matrix_h5_cooler_multiple_macro" />
c6f32406aa3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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35 <param name='pca' type="data" format="bedgraph" label="Eigenvector file" help='A PCA vector as a bedgraph file with
c6f32406aa3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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36 no header. In case of several matrices with
c6f32406aa3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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37 different conditions, ie. control
c6f32406aa3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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38 treatment, the PCA of control can be
c6f32406aa3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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39 used. Note that only one PCA can be provided.'/>
c6f32406aa3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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40 <param name='quantile' type="integer" label="Quantile" help='The number of to be used quantiles.' value="30"/>
c6f32406aa3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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41 <param name='outliers' type="float" label="Outliers" help='The number of outliers to be removed.' value="0.0"/>
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42 <param name="set_offset_value" type="text" value="" label="Offset values" optional='True'/>
c6f32406aa3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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43
c6f32406aa3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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44 <param name="image_file_format" type="select" label="Image output format">
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45 <option value="png" selected="True">png</option>
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46 <option value="svg">svg</option>
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47 <option value="pdf">pdf</option>
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48 </param>
c6f32406aa3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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49 </inputs>
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50 <outputs>
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51 <data format="png" name="outFileName" from_work_dir="plot" label="${tool.name} [${on_string}]: Plot">
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52 <change_format>
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53 <when input="image_file_format" value="svg" format="svg" />
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54 <when input="image_file_format" value="pdf" format="pdf" />
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55 </change_format>
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56 </data>
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57 <data name='output_matrix' from_work_dir='output_matrix.npz' format='binary' label='Output .npz file includes all the generated matrices'>
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58 <filter>outputMatrix == '--outputMatrix output_matrix.npz'</filter>
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59 </data>
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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="hicTransform/obs_exp_norm.h5"/>
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64 <param name="pca" value="hicCompartmentsPolarization/pca1.bedgraph"/>
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65 <output name="outFileName" file="hicCompartmentsPolarization/compartmentsPolarizationRatio.png" ftype="png" compare="sim_size"/>
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66 </test>
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67 <test>
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68 <param name="matrix_h5_cooler_multiple" value="hicTransform/obs_exp_norm.h5"/>
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69 <param name="pca" value="hicCompartmentsPolarization/pca1.bedgraph"/>
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70 <param name="quantile" value='30'/>
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71 <output name="outFileName" file="hicCompartmentsPolarization/compartmentsPolarizationRatio.png" ftype="png" compare="sim_size"/>
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72 </test>
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73 <test>
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74 <param name="matrix_h5_cooler_multiple" value="hicTransform/obs_exp_norm.h5"/>
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75 <param name="pca" value="hicCompartmentsPolarization/pca1.bedgraph"/>
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76 <param name="outliers" value='1.0'/>
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77 <output name="outFileName" file="hicCompartmentsPolarization/compartmentsPolarizationRatio.png" ftype="png" compare="sim_size"/>
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78 </test>
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79 </tests>
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80 <help><![CDATA[
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81
c6f32406aa3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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82 Comparmentalization
c6f32406aa3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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83 ===================
c6f32406aa3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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84
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85 **hicCompartmentalization** rearranges the average interaction frequencies using the first PC values to represent the global compartmentalization signal.
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86 To our knowledge this has been first introduced and implemented by Wibke Schwarzer et al. 2017 (Nature. 2017 Nov 2; 551(7678): 51–56)
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87
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88
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89 For more information about HiCExplorer please consider our documentation on readthedocs.io_.
c6f32406aa3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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90
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91 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
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92
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93 ]]></help>
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94 <expand macro="citations" />
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95 </tool>