annotate hicPCA.xml @ 16:77919cc3618e draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
author iuc
date Wed, 18 Oct 2023 10:39:52 +0000
parents 41dbf4d162a2
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1 <tool id="hicexplorer_hicpca" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
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2 <description>compute the principal components for A / B compartment analysis</description>
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3 <macros>
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4 <token name="@BINARY@">hicPCA</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 ln -s '$matrix_h5_cooler' 'matrix.$matrix_h5_cooler.ext' &&
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10 mkdir output &&
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11 @BINARY@ --matrix 'matrix.$matrix_h5_cooler.ext'
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13 @CHROMOSOME_LIST@
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15 #set $eigenvectors = ' '.join([ '\'%s\'' % $eigenvector for $eigenvector in str($whichEigenvectors).split(' ') ])
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16 --whichEigenvectors $eigenvectors
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18 #set $eigenvectors_output = ' '.join([ '\'output/pca%s.%s\'' % ($eigenvector, $outputFormat) for $eigenvector in str($whichEigenvectors).split(' ') ])
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20 --outputFileName $eigenvectors_output
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21 --format $outputFormat
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23 #if $ligation_factor:
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24 $ligation_factor
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25 #end if
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27 #if $ignoreMaskedBins:
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28 $ignoreMaskedBins
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29 #end if
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31 #if $extra_track_conditional.extra_track_selection == 'gene_density':
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32 --extraTrack '$extra_track_conditional.extraTrack'
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33 #elif $extra_track_conditional.extra_track_selection == 'histon_mark':
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34 --extraTrack '$extra_track_conditional.extraTrack'
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35 --histonMarkType '$extra_track_conditional.histonMarkType'
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36 #end if
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38 #if $pearsonMatrix:
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39 --pearsonMatrix pearson.$matrix_h5_cooler.ext
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40 #end if
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42 #if $obsexpMatrix:
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43 --obsexpMatrix obsexp.$matrix_h5_cooler.ext
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44 #end if
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46 #if $pearsonMatrix:
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47 && mv pearson.$matrix_h5_cooler.ext pearson
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48 #end if
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50 #if $obsexpMatrix:
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51 && mv obsexp.$matrix_h5_cooler.ext obsexp
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52 #end if
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54 ]]>
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55 </command>
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56 <inputs>
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57 <expand macro="matrix_h5_cooler_macro" />
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58 <param name="outputFormat" type="select" label="Output file format">
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59 <option value="bigwig" selected="true">bigwig</option>
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60 <option value="bedgraph">bedgraph</option>
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61 </param>
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62
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63 <expand macro="chromosome_list" />
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64 <param argument="--whichEigenvectors" optional="true" type="text" value="1 2" label="Eigenvectors to compute" help= "Define the eigenvectors that should be computed as a list. For example 1 2 5 to compute the first, second and fifth eigenvetor." />
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65
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66 <param name="ligation_factor" type="boolean" truevalue="--ligation_factor" label="Multiplies a scaling factor to each entry of the expected matrix to take care of the proximity ligation" />
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67 <param name="ignoreMaskedBins" type="boolean" truevalue="--ignoreMaskedBins" label="This option removes the masked bins before the PCA is computed" />
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69 <conditional name="extra_track_conditional">
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70 <param name="extra_track_selection" label="Extra track type" type="select">
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71 <option value="" selected="true">No track</option>
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72 <option value="gene_density">Gene density</option>
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73 <option value="histon_mark">Histon mark coverage</option>
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74 </param>
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75 <when value="gene_density" >
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76 <param name="extraTrack" type="data" format="bed" label="Correlate PCA with e.g. gene density or histon marks to flip sign" />
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77 </when>
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78 <when value="histon_mark">
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79 <param name="extraTrack" type="data" format="bed,bigwig" label="Correlate PCA with e.g. gene density or histon marks to flip sign" />
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80 <param name="histonMarkType" type="select" label="Histon mark type">
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81 <option value="active" selected="true">active</option>
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82 <option value="inactive">inactive</option>
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83 </param>
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84 </when>
16
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85 <when value="" />
8
b4b8343dd681 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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86 </conditional>
16
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87 <param argument="--pearsonMatrix" type="boolean" truevalue="--pearsonMatrix" falsevalue="" label="Return internally used Pearson matrix" />
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88 <param argument="--obsexpMatrix" type="boolean" truevalue="--obsexpMatrix" falsevalue="" label="Return internally used observed / expected matrix" />
8
b4b8343dd681 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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89
0
61165fbb020d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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90 </inputs>
61165fbb020d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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91 <outputs>
16
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iuc
parents: 15
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92 <data format="bedgraph" name="pca">
77919cc3618e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
iuc
parents: 15
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93 <discover_datasets pattern="__name_and_ext__" directory="output" visible="true" />
2
97c797606746 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit d76f2040a05a5f8752cbfe9a8bc1ef9efae45c01
iuc
parents: 0
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94 <change_format>
16
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iuc
parents: 15
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95 <when input="outputFormat" value="bigwig" format="bigwig" />
2
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iuc
parents: 0
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96 </change_format>
0
61165fbb020d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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97 </data>
61165fbb020d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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98
15
41dbf4d162a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa140a9f660eab2459e21b0b637b129d7de24c02
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99 <data name="pearson_outfile" from_work_dir="pearson" format="cool" label="${tool.name} on ${on_string}: Pearson matrix">
8
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100 <filter>pearsonMatrix</filter>
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101 <change_format>
15
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102 <when input_dataset="matrix_h5_cooler" attribute="ext" value="h5" format="h5"/>
8
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103 </change_format>
b4b8343dd681 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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104 </data>
15
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105 <data name="obsexp_outfile" from_work_dir="obsexp" format="cool" label="${tool.name} on ${on_string}: observed / expected matrix">
8
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106 <filter>obsexpMatrix</filter>
b4b8343dd681 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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107 <change_format>
14
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parents: 10
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108 <when input_dataset="matrix_h5_cooler" attribute="ext" value="h5" format="h5" />
8
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109 </change_format>
b4b8343dd681 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
110 </data>
0
61165fbb020d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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111 </outputs>
61165fbb020d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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112 <tests>
16
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113 <test expect_num_outputs="1">
14
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114 <param name="matrix_h5_cooler" value="small_test_matrix.cool" />
8
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115 <param name="outputFormat" value="bigwig" />
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116 <conditional name="extra_track_conditional">
14
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117 <param name="extra_track_selection" value="" />
8
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118 </conditional>
16
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diff changeset
119 <output name="pca">
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120 <discovered_dataset designation="pca1" file="hicPCA/pca1_test1.bw" ftype="bigwig" compare="sim_size" delta="100000" />
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121 <discovered_dataset designation="pca2" file="hicPCA/pca2_test1.bw" ftype="bigwig" compare="sim_size" delta="100000" />
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iuc
parents: 15
diff changeset
122 </output>
8
b4b8343dd681 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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123
b4b8343dd681 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
124 </test>
16
77919cc3618e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
iuc
parents: 15
diff changeset
125 <test expect_num_outputs="1">
14
3b5b54ed6392 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 10
diff changeset
126 <param name="matrix_h5_cooler" value="small_test_matrix.cool" />
9
3ed8e85f4f4c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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diff changeset
127 <param name="outputFormat" value="bigwig" />
3ed8e85f4f4c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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diff changeset
128 <param name="ligation_factor" value="True" />
3ed8e85f4f4c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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diff changeset
129
3ed8e85f4f4c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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diff changeset
130 <conditional name="extra_track_conditional">
14
3b5b54ed6392 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 10
diff changeset
131 <param name="extra_track_selection" value="" />
9
3ed8e85f4f4c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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diff changeset
132 </conditional>
16
77919cc3618e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
iuc
parents: 15
diff changeset
133 <output name="pca">
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iuc
parents: 15
diff changeset
134 <discovered_dataset designation="pca1" file="hicPCA/pca1_test1.bw" ftype="bigwig" compare="sim_size" delta="100000" />
77919cc3618e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
iuc
parents: 15
diff changeset
135 <discovered_dataset designation="pca2" file="hicPCA/pca2_test1.bw" ftype="bigwig" compare="sim_size" delta="100000" />
77919cc3618e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
iuc
parents: 15
diff changeset
136 </output>
9
3ed8e85f4f4c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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diff changeset
137
3ed8e85f4f4c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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diff changeset
138 </test>
16
77919cc3618e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
iuc
parents: 15
diff changeset
139 <test expect_num_outputs="1">
14
3b5b54ed6392 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 10
diff changeset
140 <param name="matrix_h5_cooler" value="small_test_matrix.cool" />
9
3ed8e85f4f4c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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diff changeset
141 <param name="outputFormat" value="bigwig" />
3ed8e85f4f4c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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diff changeset
142 <param name="ignoreMaskedBins" value="True" />
3ed8e85f4f4c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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diff changeset
143
3ed8e85f4f4c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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diff changeset
144 <conditional name="extra_track_conditional">
14
3b5b54ed6392 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 10
diff changeset
145 <param name="extra_track_selection" value="" />
9
3ed8e85f4f4c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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diff changeset
146 </conditional>
3ed8e85f4f4c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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diff changeset
147
16
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diff changeset
148 <output name="pca">
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iuc
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diff changeset
149 <discovered_dataset designation="pca1" file="hicPCA/pca1_test1.bw" ftype="bigwig" compare="sim_size" delta="100000" />
77919cc3618e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
iuc
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diff changeset
150 <discovered_dataset designation="pca2" file="hicPCA/pca2_test1.bw" ftype="bigwig" compare="sim_size" delta="100000" />
77919cc3618e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
iuc
parents: 15
diff changeset
151 </output>
9
3ed8e85f4f4c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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diff changeset
152 </test>
16
77919cc3618e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
iuc
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diff changeset
153 <test expect_num_outputs="1">
14
3b5b54ed6392 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
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diff changeset
154 <param name="matrix_h5_cooler" value="small_test_matrix.h5" />
8
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diff changeset
155 <param name="outputFormat" value="bigwig" />
b4b8343dd681 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
156 <conditional name="extra_track_conditional">
14
3b5b54ed6392 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
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diff changeset
157 <param name="extra_track_selection" value="gene_density" />
8
b4b8343dd681 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
158 <param name="extraTrack" value="dm3_genes.bed.gz" />
b4b8343dd681 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
159 </conditional>
b4b8343dd681 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
160
b4b8343dd681 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
161 <repeat name="chromosome_list">
14
3b5b54ed6392 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
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diff changeset
162 <param name="chromosomes" value="chrX" />
8
b4b8343dd681 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
163 </repeat>
b4b8343dd681 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
164 <repeat name="chromosome_list">
14
3b5b54ed6392 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
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diff changeset
165 <param name="chromosomes" value="chrXHet" />
8
b4b8343dd681 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
166 </repeat>
b4b8343dd681 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
167
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168 <output name="pca">
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169 <discovered_dataset designation="pca1" file="hicPCA/pca1_test2.bw" ftype="bigwig" compare="sim_size" delta="100000" />
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170 <discovered_dataset designation="pca2" file="hicPCA/pca2_test2.bw" ftype="bigwig" compare="sim_size" delta="100000" />
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171 </output>
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172 </test>
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173 <test expect_num_outputs="3">
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174 <param name="matrix_h5_cooler" value="small_test_matrix.h5" />
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175
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176 <param name="outputFormat" value="bigwig" />
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177 <conditional name="extra_track_conditional">
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178 <param name="extra_track_selection" value="" />
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179 </conditional>
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180 <param name="pearsonMatrix" value="True" />
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181 <param name="obsexpMatrix" value="True" />
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182
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183 <repeat name="chromosome_list">
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184 <param name="chromosomes" value="chrX" />
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185 </repeat>
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186 <repeat name="chromosome_list">
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187 <param name="chromosomes" value="chrXHet" />
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188 </repeat>
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189
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190 <output name="pca">
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191 <discovered_dataset designation="pca1" file="hicPCA/pca1_test3.bw" ftype="bigwig" compare="sim_size" delta="100000" />
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192 <discovered_dataset designation="pca2" file="hicPCA/pca2_test3.bw" ftype="bigwig" compare="sim_size" delta="100000" />
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193 </output>
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194
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195 <output name="pearson_outfile" ftype="h5">
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196 <assert_contents>
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197 <has_h5_keys keys="intervals,matrix" />
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198 </assert_contents>
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199 </output>
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200 <output name="obsexp_outfile" ftype="h5">
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201 <assert_contents>
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202 <has_h5_keys keys="intervals,matrix" />
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203 </assert_contents>
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204 </output>
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205 </test>
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206 </tests>
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207 <help><![CDATA[
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208
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209 Principal component analysis
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210 ============================
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211
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212 `Lieberman-Aiden et al. (2009)`_ demonstrated that open and closed chromatin domains throughout the genome occupy different spatial compartments in the nucleus, defined as A (activate) and B (inactive) compartments.
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213
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214 **hicPCA** computes two eigenvector files based on the input matrix for an A / B compartment analysis following the computation steps detailed by `Lieberman-Aiden et al. (2009)`_: the transformation of the contact matrix
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215 into an observed vs. expected matrix and consecutively a Pearson correlation matrix shows a plaid pattern. These plaid pattern are called A and B. Applying a PCA on the obs/exp matrix gives the eigenvectors
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216 and Lieberman-Aiden shows that the values of the eigenvectors correspond to the distribution of genes and with features of open and closed chromatin. In some cases the first principal component corresponds to the two
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217 chromosomes arms and the second eigenvector to the plaid pattern. Therefore always the first two principal components needs to be returned and investigated.
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218
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219 _________________
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220
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221 Usage
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222 -----
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223
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224 This tool must be used on Hi-C contact matrices with large bins (over 20kb) using ``hicMergeMatrixBins`` and corrected with ``hicCorrectMatrix``. Using matrices with a too high resolution (small bins or at restriction enzyme resolution) might take several days to run (even with over 100 CPU) or will fail due to memory limitations.
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225
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226 _________________
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227
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228 Output
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229 ------
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230 Two files are outputed by **hicPCA**, one with the first (pca1) and one with the second (pca2) eigenvector as bigwig or bedgraph. These files can be plotted alongside Hi-C heatmaps, gene density or external datasets such as open chromatin or histone marks enrichment using ``pyGenomeTracks`` or ``hicPlotMatrix``.
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231
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232 For example, below you can find a ``hicPlotMatrix`` of the Pearson correlation matrix derived from a contact matrix for chromosome 6 in mouse computed with ``hicTransform`` (which is part of A/B compartments computation). The optional data track at the bottom shows the first eigenvector for A/B compartment obtained using **hicPCA**.
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233
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234 .. image:: $PATH_TO_IMAGES/hicPCA.png
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235 :scale: 35 %
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236
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237 _________________
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238
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239 | For more information about HiCExplorer please consider our documentation on readthedocs.io_
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240
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241 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
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242 .. _`Lieberman-Aiden et al. (2009)`: https://pubmed.ncbi.nlm.nih.gov/19815776/
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243 ]]> </help>
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244 <expand macro="citations" />
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245 </tool>