Mercurial > repos > bgruening > hicexplorer_hicpca
annotate hicPCA.xml @ 1:d5a86de86846 draft
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 8def073a083b0619e366436a067a614555190058
author | iuc |
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date | Tue, 02 Jan 2018 10:19:28 -0500 |
parents | 61165fbb020d |
children | 97c797606746 |
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61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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1 <tool id="hicexplorer_hicpca" name="@BINARY@" version="@WRAPPER_VERSION@.0"> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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2 <description>computes the principal components for A / B compartment analysis</description> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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3 <macros> |
61165fbb020d
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> |
61165fbb020d
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> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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6 </macros> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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7 <expand macro="requirements" /> |
61165fbb020d
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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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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9 |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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10 hicPCA --matrix '$matrix_h5_cooler' |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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11 |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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12 #if $outputFormat == 'bigwig' |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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13 --outputFileName 'pca1.bigwig' 'pca2.bigwig' |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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14 --format bigwig |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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15 #elif $outputFormat == 'bedgraph' |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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16 --outputFileName 'pca1.bedgraph' 'pca2.bedgraph' |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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17 --format bedgraph |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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18 #end if |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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19 |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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20 ]]> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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21 </command> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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22 <inputs> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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23 <expand macro='matrix_h5_cooler_macro' /> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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24 <param name='outputFormat' type='select' label="Output file format"> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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25 <option value='bigwig'>bigwig</option> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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26 <option value="bedgraph">bedgraph</option> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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27 </param> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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28 |
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29 </inputs> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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30 <outputs> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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31 |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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32 <data name="pca1_bw" from_work_dir="pca1.bigwig" format="bigwig"> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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33 <filter>outputFormat == 'bigwig'</filter> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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34 </data> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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35 <data name="pca2_bw" from_work_dir="pca2.bigwig" format="bigwig"> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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36 <filter>outputFormat == 'bigwig'</filter> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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37 </data> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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38 |
61165fbb020d
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39 <data name="pca1_bedgraph" from_work_dir="pca1.bedgraph" format="bedgraph"> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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40 <filter>outputFormat == 'bedgraph'</filter> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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41 </data> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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42 <data name="pca2_bedgraph" from_work_dir="pca2.bedgraph" format="bedgraph"> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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43 <filter>outputFormat == 'bedgraph'</filter> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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44 </data> |
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45 |
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46 </outputs> |
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47 <tests> |
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48 <test> |
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49 <param name="matrix_h5_cooler" value="small_test_matrix_50kb_res.h5"/> |
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50 <param name="outputFormat" value="bedgraph" /> |
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51 <output name="pca1_bedgraph" file="pca1.bedgraph" ftype="bedgraph" compare="sim_size"/> |
61165fbb020d
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52 <output name="pca2_bedgraph" file="pca2.bedgraph" ftype="bedgraph" compare="sim_size"/> |
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53 </test> |
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54 <test> |
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55 <param name="matrix_h5_cooler" value="small_test_matrix_50kb_res.h5"/> |
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56 |
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57 <param name="outputFormat" value="bigwig" /> |
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58 <output name="pca1_bw" file="pca1.bw" ftype="bigwig" compare="sim_size"/> |
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59 <output name="pca2_bw" file="pca2.bw" ftype="bigwig" compare="sim_size"/> |
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60 </test> |
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61 </tests> |
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62 <help><![CDATA[ |
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63 Principal component analysis |
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64 ============================ |
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65 `hicPCA` computes two eigenvector files based on the input matrix for an A / B compartment analysis. |
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66 |
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67 Input |
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68 ----- |
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69 - the matrix to be analysed |
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70 |
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71 Parameters |
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72 __________ |
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73 - Output file format: bigwig or bedgraph |
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74 |
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75 Output |
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76 ------ |
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77 Two files with the first and the second eigenvector. |
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78 |
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79 | For more information about HiCExplorer please consider our documentation on readthedocs.io_ |
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80 |
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81 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html |
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82 ]]></help> |
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83 <expand macro="citations" /> |
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84 </tool> |