Mercurial > repos > bgruening > hicexplorer_hicvalidatelocations
comparison hicValidateLocations.xml @ 8:1d201e8378b3 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
author | iuc |
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date | Wed, 18 Oct 2023 11:00:15 +0000 |
parents | 662109a754b5 |
children | 11a3385e03b5 |
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7:0ecdd41d707c | 8:1d201e8378b3 |
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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 @BINARY@ | 9 @BINARY@ |
10 --data '$data' | 10 --data '$data' |
11 --protein '$protein' | 11 --validationData '$validationData' |
12 --method loops | 12 --validationType '$validationData.ext' |
13 --method $method_selector | |
13 --resolution '$resolution' | 14 --resolution '$resolution' |
14 $addChrPrefixLoops | 15 #if not $prefixLoop_selector == 'keep': |
15 $addChrPrefixProtein | 16 --chrPrefixLoops $prefixLoop_selector |
17 #end if | |
18 #if not $prefixProtein_selector == 'keep': | |
19 --chrPrefixProtein $prefixProtein_selector | |
20 #end if | |
21 | |
16 --outFileName outfile | 22 --outFileName outfile |
17 ]]> </command> | 23 ]]> </command> |
18 <inputs> | 24 <inputs> |
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." /> | 25 <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." /> |
20 <param argument="--protein" type="data" format='bed' label="Protein file" help="The protein peak file." /> | 26 <param argument="--validationData" type="data" format="bed,cool" label="Validation data" help="The protein peak file or a cool file containing e.g. HiChIP information" /> |
21 <param argument="--resolution" type="integer" value="" label="Used resolution" help='The to be binned resolution.' /> | 27 <param name="method_selector" type="select" label="Validate loop or TAD data"> |
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." /> | 28 <option value="loops" selected="True">Loops</option> |
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." /> | 29 <option value="tad">TADs</option> |
30 </param> | |
31 <param argument="--resolution" type="integer" value="" label="Used resolution" help="The to be binned resolution." /> | |
32 <param name="prefixLoop_selector" type="select" label="Add, remove, or keep the chr-prefix of the loop/TAD data"> | |
33 <option value="keep" selected="True">Keep</option> | |
34 <option value="add">Add</option> | |
35 <option value="remove">Remove</option> | |
36 | |
37 </param> | |
38 | |
39 <param name="prefixProtein_selector" type="select" label="Add, remove, or keep the chr-prefix of the validation data"> | |
40 <option value="keep" selected="True">Keep</option> | |
41 <option value="add">Add</option> | |
42 <option value="remove">Remove</option> | |
43 </param> | |
24 </inputs> | 44 </inputs> |
25 <outputs> | 45 <outputs> |
26 <data name="statistic" from_work_dir="outfile_statistics" format="bed" label="${tool.name} on [${on_string}]: Statistic" /> | 46 <data name="statistic" from_work_dir="outfile_statistics" format="bed" label="${tool.name} on [${on_string}]: Statistic" /> |
27 <data name="mergedLoops" from_work_dir="outfile_matched_locations" format="bed" label="${tool.name} on [${on_string}]: Matched locations" /> | 47 <data name="mergedLoops" from_work_dir="outfile_matched_locations" format="bed" label="${tool.name} on [${on_string}]: Matched locations" /> |
28 </outputs> | 48 </outputs> |
29 <tests> | 49 <tests> |
30 <test> | 50 <test> |
31 <param name="data" ftype='bed' value="hicValidateLocations/loops_1.bedgraph" /> | 51 <param name="data" ftype="bed" value="hicValidateLocations/loops_1.bedgraph" /> |
32 <param name="protein" ftype='bed' value="hicValidateLocations/GSM935376_hg19_Gm12878_Smc3.narrowPeak" /> | 52 <param name="validationData" ftype="bed" value="hicValidateLocations/GSM935376_hg19_Gm12878_Smc3.narrowPeak" /> |
33 <param name="resolution" value="10000" /> | 53 <param name="resolution" value="10000" /> |
34 <param name="addChrPrefixLoops" value="True" /> | 54 <param name="prefixLoop_selector" value="add" /> |
35 <output name="statistic" file="hicValidateLocations/overlap_smc3_statistics" ftype="bed" lines_diff="2" /> | 55 <output name="statistic" file="hicValidateLocations/overlap_smc3_statistics" ftype="bed" lines_diff="2" /> |
36 <output name="mergedLoops" file="hicValidateLocations/overlap_smc3_matched_locations" ftype="bed" lines_diff="4" /> | 56 <output name="mergedLoops" file="hicValidateLocations/overlap_smc3_matched_locations" ftype="bed" lines_diff="4" /> |
37 </test> | 57 </test> |
38 </tests> | 58 </tests> |
39 <help><![CDATA[ | 59 <help><![CDATA[ |