Mercurial > repos > bgruening > hicexplorer_hicvalidatelocations

annotate hicValidateLocations.xml @ 3:bccefbea9b8d draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3d3fe0c7636592f01981d491dc8ff44bb55c1750"
author iuc
date Tue, 24 Mar 2020 14:27:02 -0400
parents 61754e6c156d
children 662109a754b5
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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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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="Protein file"
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26 help="The protein peak file." />
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27 <param argument="--resolution" type="integer" value=""
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28 label="Used resolution"
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29 help='The to be binned resolution.'/>
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31 <param name='addChrPrefixLoops' type='boolean' truevalue='--addChrPrefixLoops' falsevalue="" checked="false" label="Add chr prefix to loops."
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32 help="Adding a \'chr\'-prefix to chromosome name of the loops."/>
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34 <param name='addChrPrefixProtein' type='boolean' truevalue='--addChrPrefixLoops' falsevalue="" checked="false" label="Add chr prefix to protein."
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35 help="Adding a \'chr\'-prefix to chromosome name of the protein."/>
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37 </inputs>
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38 <outputs>
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39 <data name="statistic" from_work_dir="outfile_statistics" format="bed" label="${tool.name} on [${on_string}]: Statistic"/>
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40 <data name="mergedLoops" from_work_dir="outfile_matched_locations" format="bed" label="${tool.name} on [${on_string}]: Matched locations"/>
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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="data" ftype='bed' value="hicValidateLocations/loops_1.bedgraph"/>
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45 <param name="protein" ftype='bed' value="hicValidateLocations/GSM935376_hg19_Gm12878_Smc3.narrowPeak"/>
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46 <param name="resolution" value="10000"/>
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47 <param name="addChrPrefixLoops" value="True"/>
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48 <output name="statistic" file="hicValidateLocations/overlap_smc3_statistics" ftype="bed" compare="sim_size" delta='40000'/>
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49 <output name="mergedLoops" file="hicValidateLocations/overlap_smc3_matched_locations" ftype="bed" compare="sim_size" delta='40000'/>
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50 </test>
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51 </tests>
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52 <help><![CDATA[
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54 Validate locations
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55 ==================
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57 This script overlaps the loop locations with protein locations to determine the accuracy of the loop detection.
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58 Loops need to have format as follows:
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59
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60 `chr start end chr start end`
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62 The protein peaks need to be in narrowPeaks or broadPeak format.
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63
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64 A protein match is successfull if at the bin of the x and y location a protein peak is overlapped.
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65 A bin is assumed to have a protein if one or more protein peaks falling within the bin region.
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66 The value of the protein is not considered, only match or non-match.
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67
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68 For more information about HiCExplorer please consider our documentation on readthedocs.io_
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70 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
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71 ]]></help>
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72 <expand macro="citations" />
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73 </tool>