Mercurial > repos > bgruening > hicexplorer_hicplotviewpoint

annotate hicPlotViewpoint.xml @ 2:bb82a2982d3d draft

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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
author bgruening
date Wed, 07 Mar 2018 03:41:30 -0500
parents 58d146c74d72
children 745e77f4e81e
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58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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1 <tool id="hicexplorer_hicplotviewpoint" name="@BINARY@" version="@WRAPPER_VERSION@.0">
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2 <description>computes the principal components for A / B compartment analysis</description>
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3 <macros>
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4 <token name="@BINARY@">hicPlotViewpoint</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
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10 hicPlotViewpoint --matrix '$matrix_h5_cooler'
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11 #if $interactionOutFileName:
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12 $interactionOutFileName interactions.bedgraph
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13 #end if
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14 --outFileName plot.$image_file_format
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15 --region $region
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16 --referencePoint $referencePoint
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17 && mv plot.$image_file_format plot
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18 ]]>
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19 </command>
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20 <inputs>
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21 <expand macro='matrix_h5_cooler_macro' />
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22 <expand macro="region" />
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23 <param name="referencePoint" type="text" label="Reference point"
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24 help="The format is chr:referencePoint or chr:regionStart-regionEnd."/>
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25
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26 <param name="interactionOutFileName" type="boolean" truevalue="--interactionOutFileName" falsevalue="" checked="false"
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27 label="Create bedgraph file with interactions" />
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28 <param name="image_file_format" type="select" label="Image output format">
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29 <option value="png">png</option>
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30 <option value="svg">svg</option>
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31 </param>
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32
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33 </inputs>
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34 <outputs>
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35
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36 <data format="png" name="outFileName" from_work_dir="plot">
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37 <change_format>
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38 <when input="image_file_format" value="png" format="png" />
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39 <when input="image_file_format" value="svg" format="svg" />
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40 </change_format>
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41 </data>
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42 <data name='interactionFile' from_work_dir='interactions.bedgraph' format='bedgraph'>
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43 <filter>interactionOutFileName</filter>
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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="Li_et_al_2015.h5"/>
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50 <param name="image_file_format" value="png" />
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51 <param name='region' value='X:3000000-3500000' />
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52 <param name='referencePoint' value='X:3200000' />
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53 <output name="outFileName" file="li_viewpoint_32Mb.png" ftype="png" compare="sim_size"/>
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54 </test>
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55 <test>
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56 <param name="matrix_h5_cooler" value="Li_et_al_2015.h5"/>
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57 <param name="image_file_format" value="png" />
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58 <param name='region' value='X:3000000-3500000' />
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59 <param name='referencePoint' value='X:3200000-3300000' />
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60 <param name='interactionOutFileName' value='True' />
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61 <output name="outFileName" file="li_viewpoint_32-33Mb.png" ftype="png" compare="sim_size"/>
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62 <output name="interactionFile" file="li_32-33mb_interactions.bedgraph" ftype="bedgraph" compare="sim_size"/>
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63
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64 </test>
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65 </tests>
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66 <help><![CDATA[
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67 Principal component analysis
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68 ============================
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69 `hicPCA` computes two eigenvector files based on the input matrix for an A / B compartment analysis.
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70
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71 Input
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72 -----
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73 - the matrix to be analysed
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74
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75 Parameters
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76 __________
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77 - Output file format: bigwig or bedgraph
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78
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79 Output
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80 ------
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81 Two files with the first and the second eigenvector.
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82
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83 | For more information about HiCExplorer please consider our documentation on readthedocs.io_
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84
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85 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
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86 ]]></help>
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87 <expand macro="citations" />
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88 </tool>