Mercurial > repos > bgruening > hicexplorer_hicpca

annotate hicPCA.xml @ 18:e44e72feba3e draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
author iuc
date Mon, 01 Jul 2024 19:19:35 +0000
parents 7d236f0b2298
children
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e44e72feba3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
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1 <tool id="hicexplorer_hicpca" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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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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e44e72feba3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
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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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68
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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">
e44e72feba3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
parents: 17
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81 <option value="active" selected="true">active</option>
10
b0f5c30425c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
iuc
parents: 9
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82 <option value="inactive">inactive</option>
b0f5c30425c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
iuc
parents: 9
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83 </param>
b0f5c30425c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
iuc
parents: 9
diff changeset
84 </when>
18
e44e72feba3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
parents: 17
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85 <when value="" />
10
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iuc
parents: 9
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86 </conditional>
18
e44e72feba3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
parents: 17
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87 <param argument="--pearsonMatrix" type="boolean" truevalue="--pearsonMatrix" falsevalue="" label="Return internally used Pearson matrix" />
e44e72feba3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
parents: 17
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88 <param argument="--obsexpMatrix" type="boolean" truevalue="--obsexpMatrix" falsevalue="" label="Return internally used observed / expected matrix" />
10
b0f5c30425c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
iuc
parents: 9
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89
0
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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90 </inputs>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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91 <outputs>
18
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iuc
parents: 17
diff changeset
92 <data format="bedgraph" name="pca">
e44e72feba3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
parents: 17
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93 <discover_datasets pattern="__name_and_ext__" directory="output" visible="true" />
2
cf7dbe6a2606 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit d76f2040a05a5f8752cbfe9a8bc1ef9efae45c01
iuc
parents: 0
diff changeset
94 <change_format>
18
e44e72feba3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
parents: 17
diff changeset
95 <when input="outputFormat" value="bigwig" format="bigwig" />
2
cf7dbe6a2606 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit d76f2040a05a5f8752cbfe9a8bc1ef9efae45c01
iuc
parents: 0
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96 </change_format>
0
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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97 </data>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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98
17
7d236f0b2298 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa140a9f660eab2459e21b0b637b129d7de24c02
iuc
parents: 16
diff changeset
99 <data name="pearson_outfile" from_work_dir="pearson" format="cool" label="${tool.name} on ${on_string}: Pearson matrix">
10
b0f5c30425c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
iuc
parents: 9
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100 <filter>pearsonMatrix</filter>
b0f5c30425c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
iuc
parents: 9
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101 <change_format>
17
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iuc
parents: 16
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102 <when input_dataset="matrix_h5_cooler" attribute="ext" value="h5" format="h5"/>
10
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iuc
parents: 9
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103 </change_format>
b0f5c30425c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
iuc
parents: 9
diff changeset
104 </data>
17
7d236f0b2298 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa140a9f660eab2459e21b0b637b129d7de24c02
iuc
parents: 16
diff changeset
105 <data name="obsexp_outfile" from_work_dir="obsexp" format="cool" label="${tool.name} on ${on_string}: observed / expected matrix">
10
b0f5c30425c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
iuc
parents: 9
diff changeset
106 <filter>obsexpMatrix</filter>
b0f5c30425c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
iuc
parents: 9
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107 <change_format>
16
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iuc
parents: 12
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108 <when input_dataset="matrix_h5_cooler" attribute="ext" value="h5" format="h5" />
10
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iuc
parents: 9
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109 </change_format>
b0f5c30425c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
iuc
parents: 9
diff changeset
110 </data>
0
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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111 </outputs>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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112 <tests>
18
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iuc
parents: 17
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113 <test expect_num_outputs="1">
16
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iuc
parents: 12
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114 <param name="matrix_h5_cooler" value="small_test_matrix.cool" />
10
b0f5c30425c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
iuc
parents: 9
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115 <param name="outputFormat" value="bigwig" />
b0f5c30425c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
iuc
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116 <conditional name="extra_track_conditional">
16
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iuc
parents: 12
diff changeset
117 <param name="extra_track_selection" value="" />
10
b0f5c30425c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
iuc
parents: 9
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118 </conditional>
18
e44e72feba3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
parents: 17
diff changeset
119 <output name="pca">
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iuc
parents: 17
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120 <discovered_dataset designation="pca1" file="hicPCA/pca1_test1.bw" ftype="bigwig" compare="sim_size" delta="100000" />
e44e72feba3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
parents: 17
diff changeset
121 <discovered_dataset designation="pca2" file="hicPCA/pca2_test1.bw" ftype="bigwig" compare="sim_size" delta="100000" />
e44e72feba3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
parents: 17
diff changeset
122 </output>
10
b0f5c30425c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
iuc
parents: 9
diff changeset
123
b0f5c30425c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
iuc
parents: 9
diff changeset
124 </test>
18
e44e72feba3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
parents: 17
diff changeset
125 <test expect_num_outputs="1">
16
26d661bcfe53 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 12
diff changeset
126 <param name="matrix_h5_cooler" value="small_test_matrix.cool" />
11
04d1c3d44a11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 0f4a6baff82058bb67678f402d302e2b8964f750"
iuc
parents: 10
diff changeset
127 <param name="outputFormat" value="bigwig" />
04d1c3d44a11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 0f4a6baff82058bb67678f402d302e2b8964f750"
iuc
parents: 10
diff changeset
128 <param name="ligation_factor" value="True" />
04d1c3d44a11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 0f4a6baff82058bb67678f402d302e2b8964f750"
iuc
parents: 10
diff changeset
129
04d1c3d44a11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 0f4a6baff82058bb67678f402d302e2b8964f750"
iuc
parents: 10
diff changeset
130 <conditional name="extra_track_conditional">
16
26d661bcfe53 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 12
diff changeset
131 <param name="extra_track_selection" value="" />
11
04d1c3d44a11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 0f4a6baff82058bb67678f402d302e2b8964f750"
iuc
parents: 10
diff changeset
132 </conditional>
18
e44e72feba3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
parents: 17
diff changeset
133 <output name="pca">
e44e72feba3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
parents: 17
diff changeset
134 <discovered_dataset designation="pca1" file="hicPCA/pca1_test1.bw" ftype="bigwig" compare="sim_size" delta="100000" />
e44e72feba3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
parents: 17
diff changeset
135 <discovered_dataset designation="pca2" file="hicPCA/pca2_test1.bw" ftype="bigwig" compare="sim_size" delta="100000" />
e44e72feba3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
parents: 17
diff changeset
136 </output>
11
04d1c3d44a11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 0f4a6baff82058bb67678f402d302e2b8964f750"
iuc
parents: 10
diff changeset
137
04d1c3d44a11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 0f4a6baff82058bb67678f402d302e2b8964f750"
iuc
parents: 10
diff changeset
138 </test>
18
e44e72feba3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
parents: 17
diff changeset
139 <test expect_num_outputs="1">
16
26d661bcfe53 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 12
diff changeset
140 <param name="matrix_h5_cooler" value="small_test_matrix.cool" />
11
04d1c3d44a11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 0f4a6baff82058bb67678f402d302e2b8964f750"
iuc
parents: 10
diff changeset
141 <param name="outputFormat" value="bigwig" />
04d1c3d44a11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 0f4a6baff82058bb67678f402d302e2b8964f750"
iuc
parents: 10
diff changeset
142 <param name="ignoreMaskedBins" value="True" />
04d1c3d44a11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 0f4a6baff82058bb67678f402d302e2b8964f750"
iuc
parents: 10
diff changeset
143
04d1c3d44a11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 0f4a6baff82058bb67678f402d302e2b8964f750"
iuc
parents: 10
diff changeset
144 <conditional name="extra_track_conditional">
16
26d661bcfe53 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 12
diff changeset
145 <param name="extra_track_selection" value="" />
11
04d1c3d44a11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 0f4a6baff82058bb67678f402d302e2b8964f750"
iuc
parents: 10
diff changeset
146 </conditional>
04d1c3d44a11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 0f4a6baff82058bb67678f402d302e2b8964f750"
iuc
parents: 10
diff changeset
147
18
e44e72feba3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
parents: 17
diff changeset
148 <output name="pca">
e44e72feba3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
parents: 17
diff changeset
149 <discovered_dataset designation="pca1" file="hicPCA/pca1_test1.bw" ftype="bigwig" compare="sim_size" delta="100000" />
e44e72feba3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
parents: 17
diff changeset
150 <discovered_dataset designation="pca2" file="hicPCA/pca2_test1.bw" ftype="bigwig" compare="sim_size" delta="100000" />
e44e72feba3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
parents: 17
diff changeset
151 </output>
11
04d1c3d44a11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 0f4a6baff82058bb67678f402d302e2b8964f750"
iuc
parents: 10
diff changeset
152 </test>
18
e44e72feba3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
parents: 17
diff changeset
153 <test expect_num_outputs="1">
16
26d661bcfe53 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 12
diff changeset
154 <param name="matrix_h5_cooler" value="small_test_matrix.h5" />
10
b0f5c30425c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
iuc
parents: 9
diff changeset
155 <param name="outputFormat" value="bigwig" />
b0f5c30425c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
iuc
parents: 9
diff changeset
156 <conditional name="extra_track_conditional">
16
26d661bcfe53 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 12
diff changeset
157 <param name="extra_track_selection" value="gene_density" />
10
b0f5c30425c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
iuc
parents: 9
diff changeset
158 <param name="extraTrack" value="dm3_genes.bed.gz" />
b0f5c30425c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
iuc
parents: 9
diff changeset
159 </conditional>
b0f5c30425c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
iuc
parents: 9
diff changeset
160
b0f5c30425c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
iuc
parents: 9
diff changeset
161 <repeat name="chromosome_list">
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162 <param name="chromosomes" value="chrX" />
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163 </repeat>
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164 <repeat name="chromosome_list">
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165 <param name="chromosomes" value="chrXHet" />
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166 </repeat>
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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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219 _________________
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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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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>