Mercurial > repos > bgruening > hicexplorer_chicaggregatestatistic

annotate chicAggregateStatistic.xml @ 9:affd03206adf draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 69bb60ab875c1c1769298678f0890d8b92f1899d
author iuc
date Thu, 05 Dec 2024 17:42:47 +0000
parents 554e8a6cec27
children
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1 <tool id="hicexplorer_chicaggregatestatistic" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>computes with a target file the to be tested regions for chicDifferentialTest</description>
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3 <macros>
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4 <token name="@BINARY@">chicAggregateStatistic</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 #import re
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11 @BINARY@
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13 --interactionFile '$interactionFile'
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14 --outFileName aggregatedFile.hdf5
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15 #if $targetFormat_conditional.targetFormat_selector == 'hdf5':
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16 --targetFile '$targetFormat_conditional.targetFileHDF'
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17 #else:
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18 --targetFile '$targetFormat_conditional.targetFileBED'
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19 #end if
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20 --threads @THREADS@
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22 ]]> </command>
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23 <inputs>
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24
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25 <param name="interactionFile" type="data" format="h5" label="The interaction data file created by chicViewpoint" />
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26 <conditional name="targetFormat_conditional">
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27 <param name="targetFormat_selector" type="select" label="List of chromosomes or a BED file containg regions">
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28 <option value="hdf5">Target file from chicSignificantInteractions (h5 / hdf5)</option>
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29 <option value="bed" selected="True">Regions of interest (bed)</option>
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30 </param>
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31 <when value="hdf5">
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32 <param name="targetFileHDF" type="data" format="h5" label="The target data file created by chicSignificantInteractions" />
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33 </when>
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34 <when value="bed">
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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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36 </when>
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37 </conditional>
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38 </inputs>
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39 <outputs>
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40 <data name="aggregatedFile" from_work_dir="aggregatedFile.hdf5" format="h5" label="Aggregated file" />
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41 </outputs>
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42 <tests>
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43 <test>
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44 <param name="interactionFile" value="cHi-C/chicViewpoint/two_matrices.hdf5" />
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45 <conditional name="targetFormat_conditional">
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46 <param name="targetFormat_selector" value="hdf5" />
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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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49 <output name="aggregatedFile" ftype="h5">
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50 <assert_contents>
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51 <has_h5_attribute key="type" value="aggregate" />
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52 </assert_contents>
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53 </output>
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54 </test>
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55 <test>
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56 <param name="interactionFile" value="cHi-C/chicViewpoint/two_matrices.hdf5" />
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57
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58 <conditional name="targetFormat_conditional">
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59 <param name="targetFormat_selector" value="bed" />
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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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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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71 Aggregate statistic for differential testing
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72 ============================================
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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
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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
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76 target file for all viewpoints is accepted.
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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>