Mercurial > repos > bgruening > hicexplorer_hicnormalize

annotate hicNormalize.xml @ 0:4f36f2d51d33 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
author bgruening
date Mon, 16 Dec 2019 15:47:25 -0500
parents
children 483e507c8d42
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4f36f2d51d33 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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1 <tool id="hicexplorer_hicnormalize" name="@BINARY@" version="@WRAPPER_VERSION@.0">
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2 <description>normalizes a matrix to norm range or smallest read count</description>
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3 <macros>
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4 <token name="@BINARY@">hicNormalize</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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10
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11 mkdir output &&
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12 #for $counter, $m in enumerate($matrix_h5_cooler_multiple):
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13 ln -s '$m' '${counter}_matrix.$m.ext' &&
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14 #end for
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15 #set $m = ' '.join([ '\'%s_matrix.%s\'' % ($counter, $matrix.ext) for $counter, $matrix in enumerate($matrix_h5_cooler_multiple) ])
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16 #set $m_out = ' '.join([ "'output/%s_norm_%s'" % ($counter, @ESCAPE_IDENTIFIER_MATRIX@) for $counter, $matrix in enumerate($matrix_h5_cooler_multiple) ])
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17
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18 @BINARY@ --matrices $m
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19 --normalize $normalize
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20 --outFileName $m_out
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21 ]]>
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22 </command>
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23 <inputs>
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24 <expand macro='matrix_h5_cooler_multiple_macro'/>
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25
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26 <param name='normalize' type='select' label='Normalize matrices'>
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27 <option value='norm_range'>0 to 1 range</option>
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28 <option value='smallest'>Smallest read count</option>
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29 </param>
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30
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31 </inputs>
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32 <outputs>
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33 <data name="normalize_matrix">
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34 <discover_datasets pattern="__name_and_ext__" directory="output" visible="true"/>
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35 <!-- <change_format>
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36 <when input_dataset="matrix_h5_cooler_multiple" attribute="ext" value="h5" format="h5"/>
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37 </change_format> -->
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38 </data>
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39
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40 </outputs>
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41 <tests>
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42 <test>
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43 <param name="matrix_h5_cooler_multiple" value="small_test_matrix.cool"/>
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44 <param name='normalize' value='norm_range'/>
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45 <output name="normalize_matrix">
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46 <discovered_dataset designation="0_norm_small_test_matrix" ftype="cool">
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47 <assert_contents><has_h5_keys keys="bins,chroms,indexes,pixels"/></assert_contents>
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48 </discovered_dataset>
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49 </output>
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50 </test>
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51
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52 <test>
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53 <param name="matrix_h5_cooler_multiple" value="small_test_matrix.cool,small_test_matrix.cool"/>
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54 <param name='normalize' value='smallest'/>
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55
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56 <output name="normalize_matrix">
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57 <discovered_dataset designation="0_norm_small_test_matrix" ftype="cool">
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58 <assert_contents><has_h5_keys keys="bins,chroms,indexes,pixels"/></assert_contents>
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59 </discovered_dataset>
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60 <discovered_dataset designation="1_norm_small_test_matrix" ftype="cool">
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61 <assert_contents><has_h5_keys keys="bins,chroms,indexes,pixels"/></assert_contents>
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62 </discovered_dataset>
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63 </output>
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64
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65 </test>
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66
4f36f2d51d33 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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67 <test>
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68 <param name="matrix_h5_cooler_multiple" value="small_test_matrix.h5,small_test_matrix.h5"/>
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69 <param name='normalize' value='smallest'/>
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70
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71 <output name="normalize_matrix">
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72 <discovered_dataset designation="0_norm_small_test_matrix" ftype="h5">
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73 <assert_contents><has_h5_keys keys="intervals,matrix"/></assert_contents>
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74 </discovered_dataset>
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75 <discovered_dataset designation="1_norm_small_test_matrix" ftype="h5">
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76 <assert_contents><has_h5_keys keys="intervals,matrix"/></assert_contents>
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77 </discovered_dataset>
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78 </output>
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80 </test>
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81
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82 </tests>
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83 <help><![CDATA[
4f36f2d51d33 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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84 Normalization of matrices
4f36f2d51d33 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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85 =====================================
4f36f2d51d33 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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86
4f36f2d51d33 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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87 **hicNormalize** normalizes either each matrix to a 0 - 1 value range or to the smallest read coverage.
4f36f2d51d33 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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88
4f36f2d51d33 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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89 _________________
4f36f2d51d33 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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90
4f36f2d51d33 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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91 Output
4f36f2d51d33 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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92 ------
4f36f2d51d33 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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93
4f36f2d51d33 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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94 The normalized matrices.
4f36f2d51d33 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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95
4f36f2d51d33 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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96 _________________
4f36f2d51d33 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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97
4f36f2d51d33 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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98 | For more information about HiCExplorer please consider our documentation on readthedocs.io_
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99
4f36f2d51d33 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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100 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
4f36f2d51d33 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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101 .. _`Lieberman-Aiden et al. (2009)`: https://doi.org/10.1126%2Fscience.1181369
4f36f2d51d33 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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102 ]]></help>
4f36f2d51d33 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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103 <expand macro="citations" />
4f36f2d51d33 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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104 </tool>