annotate hicNormalize.xml @ 4:e24802b3bbad draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
author iuc
date Fri, 14 Aug 2020 06:10:11 -0400
parents 483e507c8d42
children 05257e5d5016
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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
1
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19 #if $normalize_conditional.normalize == 'multiplicative':
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20 --multiplicativeValue $normalize_conditional.multiplicativeValue
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21 #end if
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22 --normalize $normalize_conditional.normalize
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23 #if $zero_threshold_value:
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24 --setToZeroThreshold $zero_threshold_value
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25 #end if
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26
0
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27 --outFileName $m_out
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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'/>
1
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32 <conditional name="normalize_conditional">
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33 <param name='normalize' type='select' label='Normalize matrices'>
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34 <option value='norm_range'>0 to 1 range</option>
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35 <option value='smallest'>Smallest read count</option>
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36 <option value='multiplicative'>Multiply by value</option>
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37 </param>
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38 <when value='norm_range'/>
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39 <when value='smallest'/>
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40 <when value='multiplicative'>
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41 <param name="multiplicativeValue" type="float" value="1.0" label="Multiplicative value"/>
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42 </when>
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43 </conditional>
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44 <param name="zero_threshold_value" type="float" value="1.0" optional='True' label="Set values below this threshold to zero"/>
0
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45 </inputs>
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46 <outputs>
1
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47 <data format='cool' name="normalize_matrix">
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48 <discover_datasets pattern="__name_and_ext__" directory="output" visible="true"/>
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49 <change_format>
0
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50 <when input_dataset="matrix_h5_cooler_multiple" attribute="ext" value="h5" format="h5"/>
1
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51 </change_format>
0
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52 </data>
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53 </outputs>
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54 <tests>
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55 <test>
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56 <param name="matrix_h5_cooler_multiple" value="small_test_matrix.cool"/>
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57 <param name='normalize' value='norm_range'/>
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58 <output name="normalize_matrix">
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59 <discovered_dataset designation="0_norm_small_test_matrix" ftype="cool">
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60 <assert_contents><has_h5_keys keys="bins,chroms,indexes,pixels"/></assert_contents>
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61 </discovered_dataset>
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62 </output>
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63 </test>
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64 <test>
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65 <param name="matrix_h5_cooler_multiple" value="small_test_matrix.cool,small_test_matrix.cool"/>
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66 <param name='normalize' value='smallest'/>
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67 <output name="normalize_matrix">
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68 <discovered_dataset designation="0_norm_small_test_matrix" ftype="cool">
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69 <assert_contents><has_h5_keys keys="bins,chroms,indexes,pixels"/></assert_contents>
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70 </discovered_dataset>
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71 <discovered_dataset designation="1_norm_small_test_matrix" ftype="cool">
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72 <assert_contents><has_h5_keys keys="bins,chroms,indexes,pixels"/></assert_contents>
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73 </discovered_dataset>
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74 </output>
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75 </test>
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76 <test>
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77 <param name="matrix_h5_cooler_multiple" value="small_test_matrix.h5,small_test_matrix.h5"/>
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78 <param name='normalize' value='smallest'/>
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79 <output name="normalize_matrix">
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80 <discovered_dataset designation="0_norm_small_test_matrix" ftype="h5">
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81 <assert_contents><has_h5_keys keys="intervals,matrix"/></assert_contents>
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82 </discovered_dataset>
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83 <discovered_dataset designation="1_norm_small_test_matrix" ftype="h5">
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84 <assert_contents><has_h5_keys keys="intervals,matrix"/></assert_contents>
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85 </discovered_dataset>
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86 </output>
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87 </test>
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88 </tests>
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89 <help><![CDATA[
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90 Normalization of matrices
1
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91 =========================
0
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92
1
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93 **hicNormalize** normalizes either each matrix to a 0 - 1 value range, to the smallest read coverage or with a user given factor.
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94
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95 _________________
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96
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97 Output
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98 ------
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99
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100 The normalized matrices.
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101
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102 _________________
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103
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104 | For more information about HiCExplorer please consider our documentation on readthedocs.io_
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105
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106 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
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107 .. _`Lieberman-Aiden et al. (2009)`: https://doi.org/10.1126%2Fscience.1181369
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108 ]]></help>
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109 <expand macro="citations" />
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110 </tool>