Mercurial > repos > bgruening > hicexplorer_hicvalidatelocations
diff hicValidateLocations.xml @ 6:662109a754b5 draft
"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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--- a/hicValidateLocations.xml Fri Dec 11 21:26:29 2020 +0000 +++ b/hicValidateLocations.xml Tue Mar 16 14:54:56 2021 +0000 @@ -1,4 +1,4 @@ -<tool id="hicexplorer_hicvalidatelocations" name="@BINARY@" version="@WRAPPER_VERSION@.0"> +<tool id="hicexplorer_hicvalidatelocations" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> <description>validate detected loops with protein peaks.</description> <macros> <token name="@BINARY@">hicValidateLocations</token> @@ -6,7 +6,6 @@ </macros> <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ - @BINARY@ --data '$data' --protein '$protein' @@ -15,38 +14,26 @@ $addChrPrefixLoops $addChrPrefixProtein --outFileName outfile - ]]></command> + ]]> </command> <inputs> - <param argument="--data" type="data" format='bed' - label="Loop file" - help="The loop file from hicDetectLoops. To use files from other sources, ' - 'please follow \'chr start end chr start end\' format." /> - <param argument="--protein" type="data" format='bed' - label="Protein file" - help="The protein peak file." /> - <param argument="--resolution" type="integer" value="" - label="Used resolution" - help='The to be binned resolution.'/> - - <param name='addChrPrefixLoops' type='boolean' truevalue='--addChrPrefixLoops' falsevalue="" checked="false" label="Add chr prefix to loops." - help="Adding a \'chr\'-prefix to chromosome name of the loops."/> - - <param name='addChrPrefixProtein' type='boolean' truevalue='--addChrPrefixLoops' falsevalue="" checked="false" label="Add chr prefix to protein." - help="Adding a \'chr\'-prefix to chromosome name of the protein."/> - + <param argument="--data" type="data" format='bed' label="Loop file" help="The loop file from hicDetectLoops. To use files from other sources, please follow 'chr start end chr start end' format." /> + <param argument="--protein" type="data" format='bed' label="Protein file" help="The protein peak file." /> + <param argument="--resolution" type="integer" value="" label="Used resolution" help='The to be binned resolution.' /> + <param argument='--addChrPrefixLoops' type='boolean' truevalue='--addChrPrefixLoops' falsevalue="" checked="false" label="Add chr prefix to loops." help="Adding a 'chr'-prefix to chromosome name of the loops." /> + <param argument='--addChrPrefixProtein' type='boolean' truevalue='--addChrPrefixProtein' falsevalue="" checked="false" label="Add chr prefix to protein." help="Adding a 'chr'-prefix to chromosome name of the protein." /> </inputs> <outputs> - <data name="statistic" from_work_dir="outfile_statistics" format="bed" label="${tool.name} on [${on_string}]: Statistic"/> - <data name="mergedLoops" from_work_dir="outfile_matched_locations" format="bed" label="${tool.name} on [${on_string}]: Matched locations"/> + <data name="statistic" from_work_dir="outfile_statistics" format="bed" label="${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'/> + <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" lines_diff="2" /> + <output name="mergedLoops" file="hicValidateLocations/overlap_smc3_matched_locations" ftype="bed" lines_diff="4" /> </test> </tests> <help><![CDATA[ @@ -68,6 +55,6 @@ For more information about HiCExplorer please consider our documentation on readthedocs.io_ .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html -]]></help> +]]> </help> <expand macro="citations" /> </tool>