Mercurial > repos > bgruening > hicexplorer_hicvalidatelocations

comparison hicValidateLocations.xml @ 6:662109a754b5 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 14:54:56 +0000
parents bccefbea9b8d
children 1d201e8378b3
comparison
equal deleted inserted replaced
5:362942f48dd2 6:662109a754b5
1 <tool id="hicexplorer_hicvalidatelocations" name="@BINARY@" version="@WRAPPER_VERSION@.0"> 1 <tool id="hicexplorer_hicvalidatelocations" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
2 <description>validate detected loops with protein peaks.</description> 2 <description>validate detected loops with protein peaks.</description>
3 <macros> 3 <macros>
4 <token name="@BINARY@">hicValidateLocations</token> 4 <token name="@BINARY@">hicValidateLocations</token>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
7 <expand macro="requirements" /> 7 <expand macro="requirements" />
8 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
9
10 @BINARY@ 9 @BINARY@
11 --data '$data' 10 --data '$data'
12 --protein '$protein' 11 --protein '$protein'
13 --method loops 12 --method loops
14 --resolution '$resolution' 13 --resolution '$resolution'
15 $addChrPrefixLoops 14 $addChrPrefixLoops
16 $addChrPrefixProtein 15 $addChrPrefixProtein
17 --outFileName outfile 16 --outFileName outfile
18 ]]></command> 17 ]]> </command>
19 <inputs> 18 <inputs>
20 <param argument="--data" type="data" format='bed' 19 <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." />
21 label="Loop file" 20 <param argument="--protein" type="data" format='bed' label="Protein file" help="The protein peak file." />
22 help="The loop file from hicDetectLoops. To use files from other sources, ' 21 <param argument="--resolution" type="integer" value="" label="Used resolution" help='The to be binned resolution.' />
23 'please follow \'chr start end chr start end\' format." /> 22 <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." />
24 <param argument="--protein" type="data" format='bed' 23 <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." />
25 label="Protein file"
26 help="The protein peak file." />
27 <param argument="--resolution" type="integer" value=""
28 label="Used resolution"
29 help='The to be binned resolution.'/>
30
31 <param name='addChrPrefixLoops' type='boolean' truevalue='--addChrPrefixLoops' falsevalue="" checked="false" label="Add chr prefix to loops."
32 help="Adding a \'chr\'-prefix to chromosome name of the loops."/>
33
34 <param name='addChrPrefixProtein' type='boolean' truevalue='--addChrPrefixLoops' falsevalue="" checked="false" label="Add chr prefix to protein."
35 help="Adding a \'chr\'-prefix to chromosome name of the protein."/>
36
37 </inputs> 24 </inputs>
38 <outputs> 25 <outputs>
39 <data name="statistic" from_work_dir="outfile_statistics" format="bed" label="${tool.name} on [${on_string}]: Statistic"/> 26 <data name="statistic" from_work_dir="outfile_statistics" format="bed" label="${tool.name} on [${on_string}]: Statistic" />
40 <data name="mergedLoops" from_work_dir="outfile_matched_locations" format="bed" label="${tool.name} on [${on_string}]: Matched locations"/> 27 <data name="mergedLoops" from_work_dir="outfile_matched_locations" format="bed" label="${tool.name} on [${on_string}]: Matched locations" />
41 </outputs> 28 </outputs>
42 <tests> 29 <tests>
43 <test> 30 <test>
44 <param name="data" ftype='bed' value="hicValidateLocations/loops_1.bedgraph"/> 31 <param name="data" ftype='bed' value="hicValidateLocations/loops_1.bedgraph" />
45 <param name="protein" ftype='bed' value="hicValidateLocations/GSM935376_hg19_Gm12878_Smc3.narrowPeak"/> 32 <param name="protein" ftype='bed' value="hicValidateLocations/GSM935376_hg19_Gm12878_Smc3.narrowPeak" />
46 <param name="resolution" value="10000"/> 33 <param name="resolution" value="10000" />
47 <param name="addChrPrefixLoops" value="True"/> 34 <param name="addChrPrefixLoops" value="True" />
48 <output name="statistic" file="hicValidateLocations/overlap_smc3_statistics" ftype="bed" compare="sim_size" delta='40000'/> 35 <output name="statistic" file="hicValidateLocations/overlap_smc3_statistics" ftype="bed" lines_diff="2" />
49 <output name="mergedLoops" file="hicValidateLocations/overlap_smc3_matched_locations" ftype="bed" compare="sim_size" delta='40000'/> 36 <output name="mergedLoops" file="hicValidateLocations/overlap_smc3_matched_locations" ftype="bed" lines_diff="4" />
50 </test> 37 </test>
51 </tests> 38 </tests>
52 <help><![CDATA[ 39 <help><![CDATA[
53 40
54 Validate locations 41 Validate locations
66 The value of the protein is not considered, only match or non-match. 53 The value of the protein is not considered, only match or non-match.
67 54
68 For more information about HiCExplorer please consider our documentation on readthedocs.io_ 55 For more information about HiCExplorer please consider our documentation on readthedocs.io_
69 56
70 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html 57 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
71 ]]></help> 58 ]]> </help>
72 <expand macro="citations" /> 59 <expand macro="citations" />
73 </tool> 60 </tool>