Mercurial > repos > bgruening > hicexplorer_hicmergeloops

comparison hicMergeLoops.xml @ 6:94b552c6830a 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 15:27:51 +0000
parents 59d3fa4c16f5
children 1511a8ebe906
comparison
equal deleted inserted replaced
5:8169710bd2fb 6:94b552c6830a
1 <tool id="hicexplorer_hicmergeloops" name="@BINARY@" version="@WRAPPER_VERSION@.0"> 1 <tool id="hicexplorer_hicmergeloops" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
2 <description>merge detected loops of different resolutions.</description> 2 <description>merge detected loops of different resolutions.</description>
3 <macros> 3 <macros>
4 <token name="@BINARY@">hicMergeLoops</token> 4 <token name="@BINARY@">hicMergeLoops</token>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
13 13
14 @BINARY@ 14 @BINARY@
15 --inputFiles $m 15 --inputFiles $m
16 --lowestResolution $lowestResolution 16 --lowestResolution $lowestResolution
17 --outFileName merged_loops.bedgraph 17 --outFileName merged_loops.bedgraph
18 ]]></command> 18 ]]> </command>
19 <inputs> 19 <inputs>
20 <param argument="--inputFiles" type="data" format='bed' 20 <param argument="--inputFiles" type="data" format='bed' multiple="true" label="Loop files to merge" help="The loop files from hicDetectLoops. To use files from other sources,
21 label="Loop files to merge" 21 please follow \'chr start end chr start end\' format and remove any header." />
22 help="The loop files from hicDetectLoops. To use files from other sources, 22 <param argument="--lowestResolution" type="integer" value="" label="Lowest used resolution" help='The lowest resolution of all loop files, i.e. 5kb, 10kb and 25kb, please use 25000.' />
23 please follow \'chr start end chr start end\' format and remove any header." multiple="true" />
24 <param argument="--lowestResolution" type="integer" value=""
25 label="Lowest used resolution"
26 help='The lowest resolution of all loop files, i.e. 5kb, 10kb and 25kb, please use 25000.'/>
27 </inputs> 23 </inputs>
28 <outputs> 24 <outputs>
29 <data name="mergedLoops" from_work_dir="merged_loops.bedgraph" format="bed" label="${tool.name} on [${on_string}]: Merged loops"/> 25 <data name="mergedLoops" from_work_dir="merged_loops.bedgraph" format="bed" label="${tool.name} on [${on_string}]: Merged loops" />
30 </outputs> 26 </outputs>
31 <tests> 27 <tests>
32 <test> 28 <test>
33 <param name="inputFiles" ftype='bed' value="hicMergeLoops/gm12878_10kb.bedgraph,hicMergeLoops/gm12878_5kb.bedgraph,hicMergeLoops/gm12878_25kb.bedgraph"/> 29 <param name="inputFiles" ftype='bed' value="hicMergeLoops/gm12878_10kb.bedgraph,hicMergeLoops/gm12878_5kb.bedgraph,hicMergeLoops/gm12878_25kb.bedgraph" />
34 <param name="lowestResolution" value="25000"/> 30 <param name="lowestResolution" value="25000" />
35 <output name="mergedLoops" file="hicMergeLoops/gm12878_all.bedgraph" ftype="bed" compare="sim_size" delta='40000'/> 31 <output name="mergedLoops" file="hicMergeLoops/gm12878_all.bedgraph" ftype="bed" />
36 </test> 32 </test>
37 </tests> 33 </tests>
38 <help><![CDATA[ 34 <help><![CDATA[
39 35
40 Merge detected loops 36 Merge detected loops
58 54
59 55
60 For more information about HiCExplorer please consider our documentation on readthedocs.io_ 56 For more information about HiCExplorer please consider our documentation on readthedocs.io_
61 57
62 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html 58 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
63 ]]></help> 59 ]]> </help>
64 <expand macro="citations" /> 60 <expand macro="citations" />
65 </tool> 61 </tool>