annotate hicCompartmentalization.xml @ 6:ed3dea19c464 draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
author iuc
date Tue, 16 Mar 2021 14:56:24 +0000
parents c6f32406aa3c
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1 <tool id="hicexplorer_hiccompartmentspolarization" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
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2 <description>compute pairwise correlations between multiple Hi-C contact matrices</description>
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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>
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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
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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@
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16 --obsexp_matrices $m
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17 --pca '$pca'
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18 --quantile $quantile
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20 #if $set_offset_value:
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21 #set $offset_array = $set_offset_value.split(' ')
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22 #set $offset = ' '.join([ '%s' % int($value) for $value in $offset_array ])
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23 --offset $offset
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24 #end if
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25 --outliers $outliers
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26 --outputFileName plot.$image_file_format
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27 && mv plot.$image_file_format plot
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28 ]]>
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29 </command>
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30 <inputs>
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31 <expand macro="matrix_h5_cooler_multiple_macro" />
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32 <param name='pca' type="data" format="bedgraph" label="Eigenvector file" help='A PCA vector as a bedgraph file with no header. In case of several matrices with
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33 different conditions, ie. control treatment, the PCA of control can be
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34 used. Note that only one PCA can be provided.' />
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35 <param name='quantile' type="integer" value="30" label="Quantile" help='The number of to be used quantiles.' />
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36 <param name='outliers' type="float" value="0.0" label="Outliers" help='The number of outliers to be removed.' />
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37 <param name="set_offset_value" type="text" optional='True' value="" label="Offset values">
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38 <validator type="expression" message="Only numeric characters and the a space as seperator are allowed.">value.replace(' ', '').isnumeric()</validator>
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39 </param>
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40
1
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41 <param name="image_file_format" type="select" label="Image output format">
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42 <option value="png" selected="True">png</option>
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43 <option value="svg">svg</option>
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44 <option value="pdf">pdf</option>
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45 </param>
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46 </inputs>
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47 <outputs>
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48 <data name="outFileName" format="png" 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="svg" format="svg" />
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51 <when input="image_file_format" value="pdf" format="pdf" />
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52 </change_format>
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53 </data>
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54 <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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55 <filter>outputMatrix == '--outputMatrix output_matrix.npz'</filter>
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56 </data>
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57 </outputs>
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58 <tests>
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59 <test>
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60 <param name="matrix_h5_cooler_multiple" value="hicTransform/obs_exp_norm.h5" />
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61 <param name="pca" value="hicCompartmentsPolarization/pca1.bedgraph" />
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62 <output name="outFileName" file="hicCompartmentsPolarization/compartmentsPolarizationRatio.png" ftype="png" compare="sim_size" />
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63 </test>
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64 <test>
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65 <param name="matrix_h5_cooler_multiple" value="hicTransform/obs_exp_norm.h5" />
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66 <param name="pca" value="hicCompartmentsPolarization/pca1.bedgraph" />
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67 <param name="quantile" value='30' />
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68 <output name="outFileName" file="hicCompartmentsPolarization/compartmentsPolarizationRatio.png" ftype="png" compare="sim_size" />
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69 </test>
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70 <test>
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71 <param name="matrix_h5_cooler_multiple" value="hicTransform/obs_exp_norm.h5" />
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72 <param name="pca" value="hicCompartmentsPolarization/pca1.bedgraph" />
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73 <param name="outliers" value='1.0' />
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74 <output name="outFileName" file="hicCompartmentsPolarization/compartmentsPolarizationRatio.png" ftype="png" compare="sim_size" />
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75 </test>
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76 </tests>
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77 <help><![CDATA[
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78
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79 Comparmentalization
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80 ===================
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81
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82 **hicCompartmentalization** rearranges the average interaction frequencies using the first PC values to represent the global compartmentalization signal.
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83 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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84
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85
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86 For more information about HiCExplorer please consider our documentation on readthedocs.io_.
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87
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88 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
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89
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90 ]]> </help>
1
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91 <expand macro="citations" />
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92 </tool>