Mercurial > repos > bgruening > hicexplorer_hicvalidatelocations

annotate hicValidateLocations.xml @ 9:11a3385e03b5 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
author iuc
date Mon, 01 Jul 2024 20:09:21 +0000
parents 1d201e8378b3
children
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11a3385e03b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
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1 <tool id="hicexplorer_hicvalidatelocations" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>validate detected loops with protein peaks.</description>
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3 <macros>
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4 <token name="@BINARY@">hicValidateLocations</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 @BINARY@
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10 --data '$data'
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11 --validationData '$validationData'
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12 --validationType '$validationData.ext'
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13 --method $method_selector
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14 --resolution '$resolution'
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15 #if not $prefixLoop_selector == 'keep':
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16 --chrPrefixLoops $prefixLoop_selector
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17 #end if
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18 #if not $prefixProtein_selector == 'keep':
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19 --chrPrefixProtein $prefixProtein_selector
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20 #end if
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21
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22 --outFileName outfile
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23 ]]> </command>
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24 <inputs>
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25 <param argument="--data" type="data" format="bed" label="Loop file" help="The loop file from hicDetectLoops. To use files from other sources, please follow 'chr start end chr start end' format." />
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26 <param argument="--validationData" type="data" format="bed,cool" label="Validation data" help="The protein peak file or a cool file containing e.g. HiChIP information" />
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27 <param name="method_selector" type="select" label="Validate loop or TAD data">
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28 <option value="loops" selected="True">Loops</option>
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29 <option value="tad">TADs</option>
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30 </param>
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31 <param argument="--resolution" type="integer" value="" label="Used resolution" help="The to be binned resolution." />
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32 <param name="prefixLoop_selector" type="select" label="Add, remove, or keep the chr-prefix of the loop/TAD data">
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33 <option value="keep" selected="True">Keep</option>
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34 <option value="add">Add</option>
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35 <option value="remove">Remove</option>
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36
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37 </param>
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38
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39 <param name="prefixProtein_selector" type="select" label="Add, remove, or keep the chr-prefix of the validation data">
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40 <option value="keep" selected="True">Keep</option>
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41 <option value="add">Add</option>
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42 <option value="remove">Remove</option>
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43 </param>
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44 </inputs>
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45 <outputs>
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46 <data name="statistic" from_work_dir="outfile_statistics" format="bed" label="${tool.name} on [${on_string}]: Statistic" />
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47 <data name="mergedLoops" from_work_dir="outfile_matched_locations" format="bed" label="${tool.name} on [${on_string}]: Matched locations" />
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48 </outputs>
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49 <tests>
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50 <test>
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51 <param name="data" ftype="bed" value="hicValidateLocations/loops_1.bedgraph" />
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52 <param name="validationData" ftype="bed" value="hicValidateLocations/GSM935376_hg19_Gm12878_Smc3.narrowPeak" />
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53 <param name="resolution" value="10000" />
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54 <param name="prefixLoop_selector" value="add" />
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55 <output name="statistic" file="hicValidateLocations/overlap_smc3_statistics" ftype="bed" lines_diff="2" />
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56 <output name="mergedLoops" file="hicValidateLocations/overlap_smc3_matched_locations" ftype="bed" lines_diff="4" />
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57 </test>
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58 </tests>
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59 <help><![CDATA[
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61 Validate locations
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62 ==================
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64 This script overlaps the loop locations with protein locations to determine the accuracy of the loop detection.
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65 Loops need to have format as follows:
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67 `chr start end chr start end`
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69 The protein peaks need to be in narrowPeaks or broadPeak format.
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71 A protein match is successfull if at the bin of the x and y location a protein peak is overlapped.
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72 A bin is assumed to have a protein if one or more protein peaks falling within the bin region.
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73 The value of the protein is not considered, only match or non-match.
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75 For more information about HiCExplorer please consider our documentation on readthedocs.io_
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77 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
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78 ]]> </help>
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79 <expand macro="citations" />
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80 </tool>