Mercurial > repos > bgruening > hicexplorer_hicmergeloops
diff hicMergeLoops.xml @ 6:94b552c6830a draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
| author | iuc |
|---|---|
| date | Tue, 16 Mar 2021 15:27:51 +0000 |
| parents | 59d3fa4c16f5 |
| children | 1511a8ebe906 |
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--- a/hicMergeLoops.xml Fri Dec 11 21:13:18 2020 +0000 +++ b/hicMergeLoops.xml Tue Mar 16 15:27:51 2021 +0000 @@ -1,4 +1,4 @@ -<tool id="hicexplorer_hicmergeloops" name="@BINARY@" version="@WRAPPER_VERSION@.0"> +<tool id="hicexplorer_hicmergeloops" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> <description>merge detected loops of different resolutions.</description> <macros> <token name="@BINARY@">hicMergeLoops</token> @@ -15,24 +15,20 @@ --inputFiles $m --lowestResolution $lowestResolution --outFileName merged_loops.bedgraph - ]]></command> + ]]> </command> <inputs> - <param argument="--inputFiles" type="data" format='bed' - label="Loop files to merge" - help="The loop files from hicDetectLoops. To use files from other sources, - please follow \'chr start end chr start end\' format and remove any header." multiple="true" /> - <param argument="--lowestResolution" type="integer" value="" - label="Lowest used resolution" - help='The lowest resolution of all loop files, i.e. 5kb, 10kb and 25kb, please use 25000.'/> + <param argument="--inputFiles" type="data" format='bed' multiple="true" label="Loop files to merge" help="The loop files from hicDetectLoops. To use files from other sources, + please follow \'chr start end chr start end\' format and remove any header." /> + <param argument="--lowestResolution" type="integer" value="" label="Lowest used resolution" help='The lowest resolution of all loop files, i.e. 5kb, 10kb and 25kb, please use 25000.' /> </inputs> <outputs> - <data name="mergedLoops" from_work_dir="merged_loops.bedgraph" format="bed" label="${tool.name} on [${on_string}]: Merged loops"/> + <data name="mergedLoops" from_work_dir="merged_loops.bedgraph" format="bed" label="${tool.name} on [${on_string}]: Merged loops" /> </outputs> <tests> <test> - <param name="inputFiles" ftype='bed' value="hicMergeLoops/gm12878_10kb.bedgraph,hicMergeLoops/gm12878_5kb.bedgraph,hicMergeLoops/gm12878_25kb.bedgraph"/> - <param name="lowestResolution" value="25000"/> - <output name="mergedLoops" file="hicMergeLoops/gm12878_all.bedgraph" ftype="bed" compare="sim_size" delta='40000'/> + <param name="inputFiles" ftype='bed' value="hicMergeLoops/gm12878_10kb.bedgraph,hicMergeLoops/gm12878_5kb.bedgraph,hicMergeLoops/gm12878_25kb.bedgraph" /> + <param name="lowestResolution" value="25000" /> + <output name="mergedLoops" file="hicMergeLoops/gm12878_all.bedgraph" ftype="bed" /> </test> </tests> <help><![CDATA[ @@ -60,6 +56,6 @@ 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>