Mercurial > repos > bgruening > hicexplorer_hicpca

annotate hicPCA.xml @ 16:26d661bcfe53 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
author iuc
date Tue, 16 Mar 2021 14:04:29 +0000
parents 6491faff4343
children 7d236f0b2298
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26d661bcfe53 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
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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' &&
b0f5c30425c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
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10 @BINARY@ --matrix 'matrix.$matrix_h5_cooler.ext'
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11
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b0f5c30425c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
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12 @CHROMOSOME_LIST@
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14 --outputFileName pca1.$outputFormat pca2.$outputFormat
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15 --format $outputFormat
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04d1c3d44a11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 0f4a6baff82058bb67678f402d302e2b8964f750"
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17 #if $ligation_factor:
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18 $ligation_factor
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19 #end if
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04d1c3d44a11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 0f4a6baff82058bb67678f402d302e2b8964f750"
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21 #if $ignoreMaskedBins:
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22 $ignoreMaskedBins
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23 #end if
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b0f5c30425c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
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25 #if $extra_track_conditional.extra_track_selection == 'gene_density':
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26 --extraTrack '$extra_track_conditional.extraTrack'
b0f5c30425c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
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27 #elif $extra_track_conditional.extra_track_selection == 'histon_mark':
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28 --extraTrack '$extra_track_conditional.extraTrack'
b0f5c30425c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
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29 --histonMarkType '$extra_track_conditional.histonMarkType'
b0f5c30425c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
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30 #end if
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b0f5c30425c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
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32 #if $pearsonMatrix:
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33 --pearsonMatrix pearson.$matrix_h5_cooler.ext
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34 #end if
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35
b0f5c30425c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
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36 #if $obsexpMatrix:
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37 --obsexpMatrix obsexp.$matrix_h5_cooler.ext
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38 #end if
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39
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40 && mv pca1.$outputFormat pca1
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41 && mv pca2.$outputFormat pca2
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42 #if $pearsonMatrix:
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43 && mv pearson.$matrix_h5_cooler.ext pearson
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44 #end if
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b0f5c30425c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
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46 #if $obsexpMatrix:
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47 && mv obsexp.$matrix_h5_cooler.ext obsexp
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48 #end if
0
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49
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50 ]]>
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51 </command>
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52 <inputs>
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53 <expand macro='matrix_h5_cooler_macro' />
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54 <param name='outputFormat' type='select' label="Output file format">
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55 <option value='bigwig' selected="true">bigwig</option>
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56 <option value="bedgraph">bedgraph</option>
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57 </param>
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58
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59 <expand macro="chromosome_list" />
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60
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61 <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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62 <param name='ignoreMaskedBins' type='boolean' truevalue='--ignoreMaskedBins' label='This option removes the masked bins before the PCA is computed' />
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63
b0f5c30425c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
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64 <conditional name="extra_track_conditional">
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65 <param name='extra_track_selection' label='Extra track type' type='select'>
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66 <option value='' selected='true'>No track</option>
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67 <option value='gene_density'>Gene density</option>
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68 <option value='histon_mark'>Histon mark coverage</option>
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69 </param>
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70 <when value='gene_density' >
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71 <param name='extraTrack' type='data' format='bed' label='Correlate PCA with e.g. gene density or histon marks to flip sign' />
10
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72 </when>
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73 <when value='histon_mark'>
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74 <param name='extraTrack' type='data' format='bed,bigwig' label='Correlate PCA with e.g. gene density or histon marks to flip sign' />
10
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75 <param name='histonMarkType' type='select' label="Histon mark type">
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76 <option value='active' selected="true">active</option>
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77 <option value="inactive">inactive</option>
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78 </param>
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79 </when>
b0f5c30425c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
iuc
parents: 9
diff changeset
80 <when value='' />
b0f5c30425c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
iuc
parents: 9
diff changeset
81 </conditional>
16
26d661bcfe53 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 12
diff changeset
82 <param argument='--pearsonMatrix' type='boolean' truevalue='--pearsonMatrix' falsevalue='' label='Return internally used Pearson matrix' />
26d661bcfe53 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 12
diff changeset
83 <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
diff changeset
84
0
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
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85 </inputs>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
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86 <outputs>
4
8682a17173fb planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 3
diff changeset
87 <data name="pca1" from_work_dir="pca1" format="bigwig" label="${tool.name} on ${matrix_h5_cooler.name} [${on_string}]: PC1">
2
cf7dbe6a2606 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit d76f2040a05a5f8752cbfe9a8bc1ef9efae45c01
iuc
parents: 0
diff changeset
88 <change_format>
cf7dbe6a2606 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit d76f2040a05a5f8752cbfe9a8bc1ef9efae45c01
iuc
parents: 0
diff changeset
89 <when input="outputFormat" value="bedgraph" format="bedgraph" />
cf7dbe6a2606 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit d76f2040a05a5f8752cbfe9a8bc1ef9efae45c01
iuc
parents: 0
diff changeset
90 </change_format>
0
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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91 </data>
16
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iuc
parents: 12
diff changeset
92 <data name="pca2" from_work_dir="pca2" format="bigwig" label="${tool.name} on ${matrix_h5_cooler.name} [${on_string}]: PC2">
2
cf7dbe6a2606 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit d76f2040a05a5f8752cbfe9a8bc1ef9efae45c01
iuc
parents: 0
diff changeset
93 <change_format>
cf7dbe6a2606 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit d76f2040a05a5f8752cbfe9a8bc1ef9efae45c01
iuc
parents: 0
diff changeset
94 <when input="outputFormat" value="bedgraph" format="bedgraph" />
cf7dbe6a2606 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit d76f2040a05a5f8752cbfe9a8bc1ef9efae45c01
iuc
parents: 0
diff changeset
95 </change_format>
0
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
96 </data>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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97
10
b0f5c30425c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
iuc
parents: 9
diff changeset
98 <data name="pearson_outfile" from_work_dir="pearson" format="cool">
b0f5c30425c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
iuc
parents: 9
diff changeset
99 <filter>pearsonMatrix</filter>
b0f5c30425c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
iuc
parents: 9
diff changeset
100 <change_format>
16
26d661bcfe53 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 12
diff changeset
101 <when input_dataset="matrix_h5_cooler" attribute="ext" value="h5" format="h5" />
10
b0f5c30425c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
iuc
parents: 9
diff changeset
102 </change_format>
b0f5c30425c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
iuc
parents: 9
diff changeset
103 </data>
b0f5c30425c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
iuc
parents: 9
diff changeset
104 <data name="obsexp_outfile" from_work_dir="obsexp" format="cool">
b0f5c30425c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
iuc
parents: 9
diff changeset
105 <filter>obsexpMatrix</filter>
b0f5c30425c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
iuc
parents: 9
diff changeset
106 <change_format>
16
26d661bcfe53 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 12
diff changeset
107 <when input_dataset="matrix_h5_cooler" attribute="ext" value="h5" format="h5" />
10
b0f5c30425c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
iuc
parents: 9
diff changeset
108 </change_format>
b0f5c30425c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
iuc
parents: 9
diff changeset
109 </data>
0
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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110 </outputs>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
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111 <tests>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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112 <test>
16
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iuc
parents: 12
diff changeset
113 <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
diff changeset
114 <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
115 <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
116 <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
diff changeset
117 </conditional>
b0f5c30425c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
iuc
parents: 9
diff changeset
118
16
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iuc
parents: 12
diff changeset
119 <output name="pca1" file="hicPCA/pca1_test1.bw" ftype="bigwig" compare="sim_size" delta='40000' />
26d661bcfe53 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 12
diff changeset
120 <output name="pca2" file="hicPCA/pca2_test1.bw" ftype="bigwig" compare="sim_size" delta='40000' />
10
b0f5c30425c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
iuc
parents: 9
diff changeset
121 </test>
b0f5c30425c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
iuc
parents: 9
diff changeset
122 <test>
16
26d661bcfe53 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 12
diff changeset
123 <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
124 <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
125 <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
126
04d1c3d44a11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 0f4a6baff82058bb67678f402d302e2b8964f750"
iuc
parents: 10
diff changeset
127 <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
128 <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
129 </conditional>
04d1c3d44a11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 0f4a6baff82058bb67678f402d302e2b8964f750"
iuc
parents: 10
diff changeset
130
16
26d661bcfe53 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 12
diff changeset
131 <output name="pca1" file="hicPCA/pca1_test1.bw" ftype="bigwig" compare="sim_size" delta='40000' />
26d661bcfe53 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 12
diff changeset
132 <output name="pca2" file="hicPCA/pca2_test1.bw" ftype="bigwig" compare="sim_size" delta='40000' />
11
04d1c3d44a11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 0f4a6baff82058bb67678f402d302e2b8964f750"
iuc
parents: 10
diff changeset
133 </test>
04d1c3d44a11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 0f4a6baff82058bb67678f402d302e2b8964f750"
iuc
parents: 10
diff changeset
134 <test>
16
26d661bcfe53 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 12
diff changeset
135 <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
136 <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
137 <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
138
04d1c3d44a11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 0f4a6baff82058bb67678f402d302e2b8964f750"
iuc
parents: 10
diff changeset
139 <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
140 <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
141 </conditional>
04d1c3d44a11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 0f4a6baff82058bb67678f402d302e2b8964f750"
iuc
parents: 10
diff changeset
142
16
26d661bcfe53 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 12
diff changeset
143 <output name="pca1" file="hicPCA/pca1_test1.bw" ftype="bigwig" compare="sim_size" delta='60000' />
26d661bcfe53 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 12
diff changeset
144 <output name="pca2" file="hicPCA/pca2_test1.bw" ftype="bigwig" compare="sim_size" delta='60000' />
11
04d1c3d44a11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 0f4a6baff82058bb67678f402d302e2b8964f750"
iuc
parents: 10
diff changeset
145 </test>
04d1c3d44a11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 0f4a6baff82058bb67678f402d302e2b8964f750"
iuc
parents: 10
diff changeset
146 <test>
16
26d661bcfe53 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 12
diff changeset
147 <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
148 <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
149 <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
150 <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
151 <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
152 </conditional>
b0f5c30425c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
iuc
parents: 9
diff changeset
153
b0f5c30425c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
iuc
parents: 9
diff changeset
154 <repeat name="chromosome_list">
16
26d661bcfe53 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 12
diff changeset
155 <param name="chromosomes" value="chrX" />
10
b0f5c30425c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
iuc
parents: 9
diff changeset
156 </repeat>
b0f5c30425c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
iuc
parents: 9
diff changeset
157 <repeat name="chromosome_list">
16
26d661bcfe53 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 12
diff changeset
158 <param name="chromosomes" value="chrXHet" />
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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159 </repeat>
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160
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161 <output name="pca1" file="hicPCA/pca1_test2.bw" ftype="bigwig" compare="sim_size" delta='40000' />
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162 <output name="pca2" file="hicPCA/pca2_test2.bw" ftype="bigwig" compare="sim_size" delta='40000' />
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163 </test>
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164 <test>
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165 <param name="matrix_h5_cooler" value="small_test_matrix.h5" />
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166
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167 <param name="outputFormat" value="bigwig" />
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168 <conditional name="extra_track_conditional">
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169 <param name="extra_track_selection" value="" />
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170 </conditional>
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171 <param name='pearsonMatrix' value='True' />
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172 <param name='obsexpMatrix' value='True' />
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173
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174 <repeat name="chromosome_list">
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175 <param name="chromosomes" value="chrX" />
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176 </repeat>
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177 <repeat name="chromosome_list">
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178 <param name="chromosomes" value="chrXHet" />
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179 </repeat>
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180
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181 <output name="pca1" file="hicPCA/pca1_test3.bw" ftype="bigwig" compare="sim_size" delta='40000' />
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182 <output name="pca2" file="hicPCA/pca2_test3.bw" ftype="bigwig" compare="sim_size" delta='40000' />
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183
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184 <output name="pearson_outfile" ftype="h5">
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185 <assert_contents>
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186 <has_h5_keys keys='intervals,matrix' />
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187 </assert_contents>
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188 </output>
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189 <output name="obsexp_outfile" ftype="h5">
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190 <assert_contents>
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191 <has_h5_keys keys='intervals,matrix' />
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192 </assert_contents>
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193 </output>
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194 </test>
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195 </tests>
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196 <help><![CDATA[
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197
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198 Principal component analysis
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199 ============================
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200
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201 `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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202
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203 **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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204 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 Pearson correlation matrix gives the eigenvectors
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205 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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206 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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207
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208 _________________
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209
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210 Usage
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211 -----
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212
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213 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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214
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215 _________________
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217 Output
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218 ------
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219 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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220
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221 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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222
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223 .. image:: $PATH_TO_IMAGES/hicPCA.png
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224 :scale: 35 %
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226 _________________
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227
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228 | For more information about HiCExplorer please consider our documentation on readthedocs.io_
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230 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
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231 .. _`Lieberman-Aiden et al. (2009)`: https://doi.org/10.1126%2Fscience.1181369
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232 ]]> </help>
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233 <expand macro="citations" />
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234 </tool>