Mercurial > repos > bgruening > hicexplorer_hicvalidatelocations

comparison hicValidateLocations.xml @ 0:f011486cbaaa draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
author bgruening
date Mon, 16 Dec 2019 14:30:02 -0500
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children 61754e6c156d
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-1:000000000000 0:f011486cbaaa
1 <tool id="hicexplorer_hicvalidatelocations" name="@BINARY@" version="@WRAPPER_VERSION@.0">
2 <description>validate detected loops with protein peaks.</description>
3 <macros>
4 <token name="@BINARY@">hicValidateLocations</token>
5 <import>macros.xml</import>
6 </macros>
7 <expand macro="requirements" />
8 <command detect_errors="exit_code"><![CDATA[
9
10 @BINARY@
11 --data '$data'
12 --protein '$protein'
13 --method loops
14 --resolution '$resolution'
15 $addChrPrefixLoops
16 $addChrPrefixProtein
17 --outFileName outfile
18 ]]></command>
19 <inputs>
20 <param argument="--data" type="data" format='bed'
21 label="Loop file"
22 help="The loop file from hicDetectLoops. To use files from other sources, '
23 'please follow \'chr start end chr start end\' format." />
24 <param argument="--protein" type="data" format='bed'
25 label="Loop file"
26 help="The loop file from hicDetectLoops. To use files from other sources, '
27 'please follow \'chr start end chr start end\' format." />
28 <param argument="--resolution" type="integer" value=""
29 label="Used resolution"
30 help='The to be binned resolution.'/>
31
32 <param name='addChrPrefixLoops' type='boolean' truevalue='--addChrPrefixLoops' falsevalue="" checked="false" label="Add chr prefix to loops."
33 help="Adding a \'chr\'-prefix to chromosome name of the loops."/>
34
35 <param name='addChrPrefixProtein' type='boolean' truevalue='--addChrPrefixLoops' falsevalue="" checked="false" label="Add chr prefix to protein."
36 help="Adding a \'chr\'-prefix to chromosome name of the protein."/>
37
38 </inputs>
39 <outputs>
40 <data name="statistic" from_work_dir="outfile_statistics" format="bed" label="${tool.name} on [${on_string}]: Statistic"/>
41 <data name="mergedLoops" from_work_dir="outfile_matched_locations" format="bed" label="${tool.name} on [${on_string}]: Matched locations"/>
42 </outputs>
43 <tests>
44 <test>
45 <param name="data" ftype='bed' value="hicValidateLocations/loops_1.bedgraph"/>
46 <param name="protein" ftype='bed' value="hicValidateLocations/GSM935376_hg19_Gm12878_Smc3.narrowPeak"/>
47 <param name="resolution" value="10000"/>
48 <param name="addChrPrefixLoops" value="True"/>
49 <output name="statistic" file="hicValidateLocations/overlap_smc3_statistics" ftype="bed" compare="sim_size" delta='40000'/>
50 <output name="mergedLoops" file="hicValidateLocations/overlap_smc3_matched_locations" ftype="bed" compare="sim_size" delta='40000'/>
51 </test>
52 </tests>
53 <help><![CDATA[
54
55 Validate locations
56 ==================
57
58 This script overlaps the loop locations with protein locations to determine the accuracy of the loop detection.
59 Loops need to have format as follows:
60
61 `chr start end chr start end`
62
63 The protein peaks need to be in narrowPeaks or broadPeak format.
64
65 A protein match is successfull if at the bin of the x and y location a protein peak is overlapped.
66 A bin is assumed to have a protein if one or more protein peaks falling within the bin region.
67 The value of the protein is not considered, only match or non-match.
68
69 For more information about HiCExplorer please consider our documentation on readthedocs.io_
70
71 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
72 ]]></help>
73 <expand macro="citations" />
74 </tool>