Mercurial > repos > bgruening > hicexplorer_hicvalidatelocations
view hicValidateLocations.xml @ 4:61cbee6f3fd0 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
author | iuc |
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date | Fri, 14 Aug 2020 05:51:42 -0400 |
parents | bccefbea9b8d |
children | 662109a754b5 |
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<tool id="hicexplorer_hicvalidatelocations" name="@BINARY@" version="@WRAPPER_VERSION@.0"> <description>validate detected loops with protein peaks.</description> <macros> <token name="@BINARY@">hicValidateLocations</token> <import>macros.xml</import> </macros> <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ @BINARY@ --data '$data' --protein '$protein' --method loops --resolution '$resolution' $addChrPrefixLoops $addChrPrefixProtein --outFileName outfile ]]></command> <inputs> <param argument="--data" type="data" format='bed' label="Loop file" help="The loop file from hicDetectLoops. To use files from other sources, ' 'please follow \'chr start end chr start end\' format." /> <param argument="--protein" type="data" format='bed' label="Protein file" help="The protein peak file." /> <param argument="--resolution" type="integer" value="" label="Used resolution" help='The to be binned resolution.'/> <param name='addChrPrefixLoops' type='boolean' truevalue='--addChrPrefixLoops' falsevalue="" checked="false" label="Add chr prefix to loops." help="Adding a \'chr\'-prefix to chromosome name of the loops."/> <param name='addChrPrefixProtein' type='boolean' truevalue='--addChrPrefixLoops' falsevalue="" checked="false" label="Add chr prefix to protein." help="Adding a \'chr\'-prefix to chromosome name of the protein."/> </inputs> <outputs> <data name="statistic" from_work_dir="outfile_statistics" format="bed" label="${tool.name} on [${on_string}]: Statistic"/> <data name="mergedLoops" from_work_dir="outfile_matched_locations" format="bed" label="${tool.name} on [${on_string}]: Matched locations"/> </outputs> <tests> <test> <param name="data" ftype='bed' value="hicValidateLocations/loops_1.bedgraph"/> <param name="protein" ftype='bed' value="hicValidateLocations/GSM935376_hg19_Gm12878_Smc3.narrowPeak"/> <param name="resolution" value="10000"/> <param name="addChrPrefixLoops" value="True"/> <output name="statistic" file="hicValidateLocations/overlap_smc3_statistics" ftype="bed" compare="sim_size" delta='40000'/> <output name="mergedLoops" file="hicValidateLocations/overlap_smc3_matched_locations" ftype="bed" compare="sim_size" delta='40000'/> </test> </tests> <help><![CDATA[ Validate locations ================== This script overlaps the loop locations with protein locations to determine the accuracy of the loop detection. Loops need to have format as follows: `chr start end chr start end` The protein peaks need to be in narrowPeaks or broadPeak format. A protein match is successfull if at the bin of the x and y location a protein peak is overlapped. A bin is assumed to have a protein if one or more protein peaks falling within the bin region. The value of the protein is not considered, only match or non-match. For more information about HiCExplorer please consider our documentation on readthedocs.io_ .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html ]]></help> <expand macro="citations" /> </tool>