Mercurial > repos > bgruening > hicexplorer_hicpca

annotate hicPCA.xml @ 12:6491faff4343 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
author iuc
date Tue, 10 Mar 2020 19:07:52 +0000
parents 04d1c3d44a11
children 26d661bcfe53
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02c7b035c9f6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
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1 <tool id="hicexplorer_hicpca" name="@BINARY@" version="@WRAPPER_VERSION@.0">
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8682a17173fb planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
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2 <description>compute the principal components for A / B compartment analysis</description>
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e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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3 <macros>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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4 <token name="@BINARY@">hicPCA</token>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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5 <import>macros.xml</import>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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6 </macros>
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7 <expand macro="requirements" />
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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8 <command detect_errors="exit_code"><![CDATA[
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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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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.$matrix_h5_cooler.ext'
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e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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11
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b0f5c30425c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
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12 @CHROMOSOME_LIST@
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cf7dbe6a2606 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit d76f2040a05a5f8752cbfe9a8bc1ef9efae45c01
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14 --outputFileName pca1.$outputFormat pca2.$outputFormat
cf7dbe6a2606 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit d76f2040a05a5f8752cbfe9a8bc1ef9efae45c01
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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:
04d1c3d44a11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 0f4a6baff82058bb67678f402d302e2b8964f750"
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18 $ligation_factor
04d1c3d44a11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 0f4a6baff82058bb67678f402d302e2b8964f750"
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19 #end if
04d1c3d44a11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 0f4a6baff82058bb67678f402d302e2b8964f750"
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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:
04d1c3d44a11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 0f4a6baff82058bb67678f402d302e2b8964f750"
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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 $extra_track_conditional.extra_track_selection == 'gene_density':
b0f5c30425c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
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26 --extraTrack '$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 $extra_track_conditional.extra_track_selection == 'histon_mark':
b0f5c30425c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
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28 --extraTrack '$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
b0f5c30425c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
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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
b0f5c30425c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
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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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36 #if $obsexpMatrix:
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37 --obsexpMatrix obsexp.$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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38 #end if
b0f5c30425c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
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39
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40 && mv pca1.$outputFormat pca1
cf7dbe6a2606 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit d76f2040a05a5f8752cbfe9a8bc1ef9efae45c01
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41 && mv pca2.$outputFormat pca2
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42 #if $pearsonMatrix:
b0f5c30425c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
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43 && mv pearson.$matrix_h5_cooler.ext pearson
b0f5c30425c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
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44 #end if
b0f5c30425c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
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45
b0f5c30425c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
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46 #if $obsexpMatrix:
b0f5c30425c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
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47 && mv obsexp.$matrix_h5_cooler.ext obsexp
b0f5c30425c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
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48 #end if
0
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49
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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50 ]]>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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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" />
b0f5c30425c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
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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'/>
04d1c3d44a11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 0f4a6baff82058bb67678f402d302e2b8964f750"
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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>
b0f5c30425c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
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68 <option value='histon_mark'>Histon mark coverage</option>
b0f5c30425c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
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69 </param>
b0f5c30425c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
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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'/>
b0f5c30425c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
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72 </when>
b0f5c30425c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
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73 <when value='histon_mark'>
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74 <param name='extraTrack' type='data' format='bed' label='Correlate PCA with e.g. gene density or histon marks to flip sign'/>
b0f5c30425c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
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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>
b0f5c30425c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
iuc
parents: 9
diff changeset
82
b0f5c30425c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
iuc
parents: 9
diff changeset
83 <param name='pearsonMatrix' type='boolean' truevalue='--pearsonMatrix' falsevalue='' label='Return internally used Pearson matrix'/>
b0f5c30425c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
iuc
parents: 9
diff changeset
84 <param name='obsexpMatrix' type='boolean' truevalue='--obsexpMatrix' falsevalue='' label='Return internally used observed / expected matrix'/>
b0f5c30425c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
iuc
parents: 9
diff changeset
85
0
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
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diff changeset
86 </inputs>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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diff changeset
87 <outputs>
4
8682a17173fb planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 3
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88 <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
89 <change_format>
cf7dbe6a2606 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit d76f2040a05a5f8752cbfe9a8bc1ef9efae45c01
iuc
parents: 0
diff changeset
90 <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
91 </change_format>
0
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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92 </data>
4
8682a17173fb planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 3
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93 <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
94 <change_format>
cf7dbe6a2606 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit d76f2040a05a5f8752cbfe9a8bc1ef9efae45c01
iuc
parents: 0
diff changeset
95 <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
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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diff changeset
97 </data>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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98
10
b0f5c30425c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
iuc
parents: 9
diff changeset
99 <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
100 <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
101 <change_format>
b0f5c30425c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
iuc
parents: 9
diff changeset
102 <when input_dataset="matrix_h5_cooler" attribute="ext" value="h5" format="h5"/>
b0f5c30425c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
iuc
parents: 9
diff changeset
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>
b0f5c30425c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
iuc
parents: 9
diff changeset
105 <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
106 <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
107 <change_format>
b0f5c30425c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
iuc
parents: 9
diff changeset
108 <when input_dataset="matrix_h5_cooler" attribute="ext" value="h5" format="h5"/>
b0f5c30425c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
iuc
parents: 9
diff changeset
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>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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113 <test>
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="matrix_h5_cooler" value="small_test_matrix.cool"/>
b0f5c30425c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
iuc
parents: 9
diff changeset
115 <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
116 <conditional name="extra_track_conditional">
b0f5c30425c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
iuc
parents: 9
diff changeset
117 <param name="extra_track_selection" value=""/>
b0f5c30425c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
iuc
parents: 9
diff changeset
118 </conditional>
b0f5c30425c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
iuc
parents: 9
diff changeset
119
b0f5c30425c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
iuc
parents: 9
diff changeset
120 <output name="pca1" file="hicPCA/pca1_test1.bw" ftype="bigwig" compare="sim_size" delta='40000'/>
b0f5c30425c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
iuc
parents: 9
diff changeset
121 <output name="pca2" file="hicPCA/pca2_test1.bw" ftype="bigwig" compare="sim_size" delta='40000'/>
b0f5c30425c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
iuc
parents: 9
diff changeset
122 </test>
b0f5c30425c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
iuc
parents: 9
diff changeset
123 <test>
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="matrix_h5_cooler" value="small_test_matrix.cool"/>
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="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
126 <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
127
04d1c3d44a11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 0f4a6baff82058bb67678f402d302e2b8964f750"
iuc
parents: 10
diff changeset
128 <conditional name="extra_track_conditional">
04d1c3d44a11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 0f4a6baff82058bb67678f402d302e2b8964f750"
iuc
parents: 10
diff changeset
129 <param name="extra_track_selection" value=""/>
04d1c3d44a11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 0f4a6baff82058bb67678f402d302e2b8964f750"
iuc
parents: 10
diff changeset
130 </conditional>
04d1c3d44a11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 0f4a6baff82058bb67678f402d302e2b8964f750"
iuc
parents: 10
diff changeset
131
04d1c3d44a11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 0f4a6baff82058bb67678f402d302e2b8964f750"
iuc
parents: 10
diff changeset
132 <output name="pca1" file="hicPCA/pca1_test1.bw" ftype="bigwig" compare="sim_size" delta='40000'/>
04d1c3d44a11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 0f4a6baff82058bb67678f402d302e2b8964f750"
iuc
parents: 10
diff changeset
133 <output name="pca2" file="hicPCA/pca2_test1.bw" ftype="bigwig" compare="sim_size" delta='40000'/>
04d1c3d44a11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 0f4a6baff82058bb67678f402d302e2b8964f750"
iuc
parents: 10
diff changeset
134 </test>
04d1c3d44a11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 0f4a6baff82058bb67678f402d302e2b8964f750"
iuc
parents: 10
diff changeset
135 <test>
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="matrix_h5_cooler" value="small_test_matrix.cool"/>
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="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
138 <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
139
04d1c3d44a11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 0f4a6baff82058bb67678f402d302e2b8964f750"
iuc
parents: 10
diff changeset
140 <conditional name="extra_track_conditional">
04d1c3d44a11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 0f4a6baff82058bb67678f402d302e2b8964f750"
iuc
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diff changeset
141 <param name="extra_track_selection" value=""/>
04d1c3d44a11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 0f4a6baff82058bb67678f402d302e2b8964f750"
iuc
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diff changeset
142 </conditional>
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 <output name="pca1" file="hicPCA/pca1_test1.bw" ftype="bigwig" compare="sim_size" delta='60000'/>
04d1c3d44a11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 0f4a6baff82058bb67678f402d302e2b8964f750"
iuc
parents: 10
diff changeset
145 <output name="pca2" file="hicPCA/pca2_test1.bw" ftype="bigwig" compare="sim_size" delta='60000'/>
04d1c3d44a11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 0f4a6baff82058bb67678f402d302e2b8964f750"
iuc
parents: 10
diff changeset
146 </test>
04d1c3d44a11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 0f4a6baff82058bb67678f402d302e2b8964f750"
iuc
parents: 10
diff changeset
147 <test>
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="matrix_h5_cooler" value="small_test_matrix.h5"/>
b0f5c30425c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
iuc
parents: 9
diff changeset
149 <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
150 <conditional name="extra_track_conditional">
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="extra_track_selection" value="gene_density"/>
b0f5c30425c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
iuc
parents: 9
diff changeset
152 <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
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diff changeset
153 </conditional>
b0f5c30425c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
iuc
parents: 9
diff changeset
154
b0f5c30425c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
iuc
parents: 9
diff changeset
155 <repeat name="chromosome_list">
b0f5c30425c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
iuc
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diff changeset
156 <param name="chromosomes" value="chrX"/>
b0f5c30425c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
iuc
parents: 9
diff changeset
157 </repeat>
b0f5c30425c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
iuc
parents: 9
diff changeset
158 <repeat name="chromosome_list">
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 <param name="chromosomes" value="chrXHet"/>
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160 </repeat>
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161
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162 <output name="pca1" file="hicPCA/pca1_test2.bw" ftype="bigwig" compare="sim_size" delta='40000'/>
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163 <output name="pca2" file="hicPCA/pca2_test2.bw" ftype="bigwig" compare="sim_size" delta='40000'/>
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164 </test>
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165 <test>
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166 <param name="matrix_h5_cooler" value="small_test_matrix.h5"/>
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167
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168 <param name="outputFormat" value="bigwig" />
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169 <conditional name="extra_track_conditional">
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170 <param name="extra_track_selection" value=""/>
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171 </conditional>
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172 <param name='pearsonMatrix' value='True'/>
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173 <param name='obsexpMatrix' value='True'/>
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174
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175 <repeat name="chromosome_list">
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176 <param name="chromosomes" value="chrX"/>
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177 </repeat>
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178 <repeat name="chromosome_list">
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179 <param name="chromosomes" value="chrXHet"/>
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180 </repeat>
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181
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182 <output name="pca1" file="hicPCA/pca1_test3.bw" ftype="bigwig" compare="sim_size" delta='40000'/>
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183 <output name="pca2" file="hicPCA/pca2_test3.bw" ftype="bigwig" compare="sim_size" delta='40000'/>
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184
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185 <output name="pearson_outfile" ftype="h5">
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186 <assert_contents>
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187 <has_h5_keys keys='intervals,matrix'/>
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188 </assert_contents>
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189 </output>
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190 <output name="obsexp_outfile" ftype="h5">
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191 <assert_contents>
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192 <has_h5_keys keys='intervals,matrix'/>
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193 </assert_contents>
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194 </output>
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195 </test>
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196 </tests>
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197 <help><![CDATA[
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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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229
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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>