Mercurial > repos > bgruening > hicexplorer_hicnormalize

annotate hicNormalize.xml @ 8:6d042c96aceb draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
author iuc
date Wed, 18 Oct 2023 10:21:43 +0000
parents 8ad23dfdaabb
children f34ab9882252
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1 <tool id="hicexplorer_hicnormalize" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
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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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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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18 @BINARY@ --matrices $m
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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" />
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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" />
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45 </inputs>
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46 <outputs>
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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" />
1
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49 <change_format>
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50 <when input_dataset="matrix_h5_cooler_multiple" attribute="ext" value="h5" format="h5" />
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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>
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61 <has_h5_keys keys="bins,chroms,indexes,pixels" />
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62 </assert_contents>
0
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63 </discovered_dataset>
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64 </output>
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65 </test>
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66 <test>
6
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67 <param name="matrix_h5_cooler_multiple" value="small_test_matrix.cool,small_test_matrix.cool" />
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68 <param name="normalize" value="smallest" />
0
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69 <output name="normalize_matrix">
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70 <discovered_dataset designation="0_norm_small_test_matrix" ftype="cool">
6
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71 <assert_contents>
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72 <has_h5_keys keys="bins,chroms,indexes,pixels" />
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73 </assert_contents>
0
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74 </discovered_dataset>
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75 <discovered_dataset designation="1_norm_small_test_matrix" ftype="cool">
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76 <assert_contents>
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77 <has_h5_keys keys="bins,chroms,indexes,pixels" />
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78 </assert_contents>
0
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79 </discovered_dataset>
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80 </output>
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81 </test>
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82 <test>
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83 <param name="matrix_h5_cooler_multiple" value="small_test_matrix.h5,small_test_matrix.h5" />
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84 <param name="normalize" value="smallest" />
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85 <output name="normalize_matrix">
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86 <discovered_dataset designation="0_norm_small_test_matrix" ftype="h5">
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87 <assert_contents>
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88 <has_h5_keys keys="intervals,matrix" />
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89 </assert_contents>
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90 </discovered_dataset>
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91 <discovered_dataset designation="1_norm_small_test_matrix" ftype="h5">
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92 <assert_contents>
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93 <has_h5_keys keys="intervals,matrix" />
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94 </assert_contents>
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95 </discovered_dataset>
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96 </output>
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97 </test>
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98 </tests>
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99 <help><![CDATA[
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100
0
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101 Normalization of matrices
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102 =========================
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103
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104 **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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105
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106 _________________
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107
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108 Output
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109 ------
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110
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111 The normalized matrices.
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112
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113 _________________
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114
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115 | For more information about HiCExplorer please consider our documentation on readthedocs.io_
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116
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117 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
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118 .. _`Lieberman-Aiden et al. (2009)`: https://pubmed.ncbi.nlm.nih.gov/19815776/
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119 ]]> </help>
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120 <expand macro="citations" />
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121 </tool>