Mercurial > repos > bgruening > hicexplorer_hicvalidatelocations

annotate hicValidateLocations.xml @ 0:f011486cbaaa draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
author bgruening
date Mon, 16 Dec 2019 14:30:02 -0500
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children 61754e6c156d
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0
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1 <tool id="hicexplorer_hicvalidatelocations" name="@BINARY@" version="@WRAPPER_VERSION@.0">
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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
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10 @BINARY@
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11 --data '$data'
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12 --protein '$protein'
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13 --method loops
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14 --resolution '$resolution'
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15 $addChrPrefixLoops
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16 $addChrPrefixProtein
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17 --outFileName outfile
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18 ]]></command>
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19 <inputs>
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20 <param argument="--data" type="data" format='bed'
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21 label="Loop file"
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22 help="The loop file from hicDetectLoops. To use files from other sources, '
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23 'please follow \'chr start end chr start end\' format." />
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24 <param argument="--protein" type="data" format='bed'
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25 label="Loop file"
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26 help="The loop file from hicDetectLoops. To use files from other sources, '
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27 'please follow \'chr start end chr start end\' format." />
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28 <param argument="--resolution" type="integer" value=""
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29 label="Used resolution"
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30 help='The to be binned resolution.'/>
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31
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32 <param name='addChrPrefixLoops' type='boolean' truevalue='--addChrPrefixLoops' falsevalue="" checked="false" label="Add chr prefix to loops."
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33 help="Adding a \'chr\'-prefix to chromosome name of the loops."/>
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34
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35 <param name='addChrPrefixProtein' type='boolean' truevalue='--addChrPrefixLoops' falsevalue="" checked="false" label="Add chr prefix to protein."
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36 help="Adding a \'chr\'-prefix to chromosome name of the protein."/>
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37
f011486cbaaa "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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38 </inputs>
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39 <outputs>
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40 <data name="statistic" from_work_dir="outfile_statistics" format="bed" label="${tool.name} on [${on_string}]: Statistic"/>
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41 <data name="mergedLoops" from_work_dir="outfile_matched_locations" format="bed" label="${tool.name} on [${on_string}]: Matched locations"/>
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42 </outputs>
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43 <tests>
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44 <test>
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45 <param name="data" ftype='bed' value="hicValidateLocations/loops_1.bedgraph"/>
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46 <param name="protein" ftype='bed' value="hicValidateLocations/GSM935376_hg19_Gm12878_Smc3.narrowPeak"/>
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47 <param name="resolution" value="10000"/>
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48 <param name="addChrPrefixLoops" value="True"/>
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49 <output name="statistic" file="hicValidateLocations/overlap_smc3_statistics" ftype="bed" compare="sim_size" delta='40000'/>
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50 <output name="mergedLoops" file="hicValidateLocations/overlap_smc3_matched_locations" ftype="bed" compare="sim_size" delta='40000'/>
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51 </test>
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52 </tests>
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53 <help><![CDATA[
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54
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55 Validate locations
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56 ==================
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57
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58 This script overlaps the loop locations with protein locations to determine the accuracy of the loop detection.
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59 Loops need to have format as follows:
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60
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61 `chr start end chr start end`
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62
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63 The protein peaks need to be in narrowPeaks or broadPeak format.
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64
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65 A protein match is successfull if at the bin of the x and y location a protein peak is overlapped.
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66 A bin is assumed to have a protein if one or more protein peaks falling within the bin region.
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67 The value of the protein is not considered, only match or non-match.
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68
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69 For more information about HiCExplorer please consider our documentation on readthedocs.io_
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70
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71 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
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72 ]]></help>
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73 <expand macro="citations" />
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74 </tool>