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annotate hicValidateLocations.xml @ 6:662109a754b5 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
author iuc
date Tue, 16 Mar 2021 14:54:56 +0000
parents bccefbea9b8d
children 1d201e8378b3
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662109a754b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
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1 <tool id="hicexplorer_hicvalidatelocations" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
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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 '$data'
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11 --protein '$protein'
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12 --method loops
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13 --resolution '$resolution'
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14 $addChrPrefixLoops
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15 $addChrPrefixProtein
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16 --outFileName outfile
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17 ]]> </command>
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18 <inputs>
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19 <param argument="--data" type="data" format='bed' label="Loop file" help="The loop file from hicDetectLoops. To use files from other sources, please follow 'chr start end chr start end' format." />
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20 <param argument="--protein" type="data" format='bed' label="Protein file" help="The protein peak file." />
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21 <param argument="--resolution" type="integer" value="" label="Used resolution" help='The to be binned resolution.' />
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22 <param argument='--addChrPrefixLoops' type='boolean' truevalue='--addChrPrefixLoops' falsevalue="" checked="false" label="Add chr prefix to loops." help="Adding a 'chr'-prefix to chromosome name of the loops." />
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23 <param argument='--addChrPrefixProtein' type='boolean' truevalue='--addChrPrefixProtein' falsevalue="" checked="false" label="Add chr prefix to protein." help="Adding a 'chr'-prefix to chromosome name of the protein." />
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24 </inputs>
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25 <outputs>
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26 <data name="statistic" from_work_dir="outfile_statistics" format="bed" label="${tool.name} on [${on_string}]: Statistic" />
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27 <data name="mergedLoops" from_work_dir="outfile_matched_locations" format="bed" label="${tool.name} on [${on_string}]: Matched locations" />
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28 </outputs>
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29 <tests>
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30 <test>
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31 <param name="data" ftype='bed' value="hicValidateLocations/loops_1.bedgraph" />
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32 <param name="protein" ftype='bed' value="hicValidateLocations/GSM935376_hg19_Gm12878_Smc3.narrowPeak" />
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33 <param name="resolution" value="10000" />
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34 <param name="addChrPrefixLoops" value="True" />
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35 <output name="statistic" file="hicValidateLocations/overlap_smc3_statistics" ftype="bed" lines_diff="2" />
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36 <output name="mergedLoops" file="hicValidateLocations/overlap_smc3_matched_locations" ftype="bed" lines_diff="4" />
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37 </test>
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38 </tests>
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39 <help><![CDATA[
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41 Validate locations
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42 ==================
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44 This script overlaps the loop locations with protein locations to determine the accuracy of the loop detection.
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45 Loops need to have format as follows:
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47 `chr start end chr start end`
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49 The protein peaks need to be in narrowPeaks or broadPeak format.
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51 A protein match is successfull if at the bin of the x and y location a protein peak is overlapped.
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52 A bin is assumed to have a protein if one or more protein peaks falling within the bin region.
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53 The value of the protein is not considered, only match or non-match.
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55 For more information about HiCExplorer please consider our documentation on readthedocs.io_
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57 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
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58 ]]> </help>
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59 <expand macro="citations" />
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60 </tool>