Mercurial > repos > bgruening > hicexplorer_chicaggregatestatistic
annotate chicAggregateStatistic.xml @ 10:952abbc4b1de draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 79133bc3739fbcc6c2055d589679aae312161d03
author | iuc |
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date | Mon, 04 Nov 2024 23:59:07 +0000 |
parents | fb7068d30ec9 |
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fb7068d30ec9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
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1 <tool id="hicexplorer_chicaggregatestatistic" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> |
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ee745fbe9f14
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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2 <description>computes with a target file the to be tested regions for chicDifferentialTest</description> |
ee745fbe9f14
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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3 <macros> |
ee745fbe9f14
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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4 <token name="@BINARY@">chicAggregateStatistic</token> |
ee745fbe9f14
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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5 <import>macros.xml</import> |
ee745fbe9f14
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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6 </macros> |
ee745fbe9f14
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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7 <expand macro="requirements" /> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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8 <command detect_errors="exit_code"><![CDATA[ |
ee745fbe9f14
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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9 #import re |
8
01c37e54e86e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
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10 |
01c37e54e86e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
iuc
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11 @BINARY@ |
01c37e54e86e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
iuc
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12 |
01c37e54e86e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
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13 --interactionFile '$interactionFile' |
01c37e54e86e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
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14 --outFileName aggregatedFile.hdf5 |
01c37e54e86e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
iuc
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15 #if $targetFormat_conditional.targetFormat_selector == 'hdf5': |
01c37e54e86e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
iuc
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16 --targetFile '$targetFormat_conditional.targetFileHDF' |
01c37e54e86e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
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17 #else: |
01c37e54e86e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
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18 --targetFile '$targetFormat_conditional.targetFileBED' |
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d6f5e51e97ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
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19 #end if |
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ee745fbe9f14
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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20 --threads @THREADS@ |
ee745fbe9f14
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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21 |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
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22 ]]> </command> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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23 <inputs> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
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24 |
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01c37e54e86e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
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25 <param name="interactionFile" type="data" format="h5" label="The interaction data file created by chicViewpoint" /> |
01c37e54e86e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
iuc
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26 <conditional name="targetFormat_conditional"> |
01c37e54e86e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
iuc
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27 <param name="targetFormat_selector" type="select" label="List of chromosomes or a BED file containg regions"> |
01c37e54e86e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
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28 <option value="hdf5">Target file from chicSignificantInteractions (h5 / hdf5)</option> |
01c37e54e86e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
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29 <option value="bed" selected="True">Regions of interest (bed)</option> |
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d6f5e51e97ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
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30 </param> |
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01c37e54e86e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
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31 <when value="hdf5"> |
01c37e54e86e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
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32 <param name="targetFileHDF" type="data" format="h5" label="The target data file created by chicSignificantInteractions" /> |
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d6f5e51e97ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
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33 </when> |
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01c37e54e86e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
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34 <when value="bed"> |
01c37e54e86e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
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35 <param name="targetFileBED" type="data" format="bed" label="Regions of interest" help="BED file which stores a list of regions that are used to aggregate the data for the differntial test." /> |
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d6f5e51e97ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
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36 </when> |
d6f5e51e97ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
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37 </conditional> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
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38 </inputs> |
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39 <outputs> |
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01c37e54e86e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
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40 <data name="aggregatedFile" from_work_dir="aggregatedFile.hdf5" format="h5" label="Aggregated file" /> |
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ee745fbe9f14
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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41 </outputs> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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42 <tests> |
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43 <test> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
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44 <param name="interactionFile" value="cHi-C/chicViewpoint/two_matrices.hdf5" /> |
01c37e54e86e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
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45 <conditional name="targetFormat_conditional"> |
01c37e54e86e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
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46 <param name="targetFormat_selector" value="hdf5" /> |
01c37e54e86e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
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47 <param name="targetFileHDF" value="cHi-C/chicSignificantInteractions/targetFile_dual.hdf5" /> |
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48 </conditional> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
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49 <output name="aggregatedFile" ftype="h5"> |
01c37e54e86e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
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50 <assert_contents> |
01c37e54e86e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
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51 <has_h5_attribute key="type" value="aggregate" /> |
01c37e54e86e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
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52 </assert_contents> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
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53 </output> |
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54 </test> |
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55 <test> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
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56 <param name="interactionFile" value="cHi-C/chicViewpoint/two_matrices.hdf5" /> |
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57 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
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58 <conditional name="targetFormat_conditional"> |
01c37e54e86e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
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59 <param name="targetFormat_selector" value="bed" /> |
01c37e54e86e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
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60 <param name="targetFileBED" value="cHi-C/target_list.bed" /> |
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61 </conditional> |
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62 <output name="aggregatedFile" ftype="h5"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
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63 <assert_contents> |
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64 <has_h5_attribute key="type" value="aggregate" /> |
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65 </assert_contents> |
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66 </output> |
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67 </test> |
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68 </tests> |
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69 <help><![CDATA[ |
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70 |
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71 Aggregate statistic for differential testing |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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72 ============================================ |
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73 |
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74 chicAggregateStatistic is a preprocessing tool for chicDifferentialTest. It takes two consecutive viewpoint files and one target file and creates one |
ee745fbe9f14
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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75 file containing all locations which should be tested for differential interactions. Either one target file for two consecutive viewpoint files or one |
ee745fbe9f14
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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76 target file for all viewpoints is accepted. |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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78 For more information about HiCExplorer please consider our documentation on readthedocs.io_ |
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80 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html |
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81 ]]> </help> |
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82 <expand macro="citations" /> |
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83 </tool> |