# HG changeset patch # User rnateam # Date 1481891767 18000 # Node ID 165fe96228be35397574a7c4ff34757b7470f779 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit 21aaee40723b5341b4236edeb0e72995c2054053 diff -r 000000000000 -r 165fe96228be NSPDK_candidateClusters.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NSPDK_candidateClusters.xml Fri Dec 16 07:36:07 2016 -0500 @@ -0,0 +1,149 @@ + + + graphclust-wrappers + perl-array-utils + nspdk + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + iteration_num['iteration_num_selector'] is False + + + iteration_num['iteration_num_selector'] is False + + + iteration_num['iteration_num_selector'] is False + + + iteration_num['iteration_num_selector'] is True + + + iteration_num['iteration_num_selector'] is True + + + iteration_num['iteration_num_selector'] is True + + + + + + + + + + + + + + + + + + + + + + + + + + + + (default: 10) + ++ **-otknn** : flag to output true (i.e. implies full kernel matrix evaluation) k-nearest neighburs (default: 0) + ++ **-oc** : flag to output clusters (default: 0) + ++ **-nhf** : for the Locality Sensitive Hashing function (default: 250) + ++ **-ensf** : (default: 10) (0 to avoid trimming) + ++ **-usn** : use shared neighbourhood to weight center density (default: 0) + + + ]]> + + + 10.1093/bioinformatics/bts224 + @inproceedings{costa2010fast, + title={Fast neighborhood subgraph pairwise distance kernel}, + author={Costa, Fabrizio and De Grave, Kurt}, + booktitle={Proceedings of the 26th International Conference on Machine Learning}, + pages={255--262}, + year={2010}, + organization={Omnipress} + } + + + diff -r 000000000000 -r 165fe96228be NSPDK_sparseVect.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NSPDK_sparseVect.xml Fri Dec 16 07:36:07 2016 -0500 @@ -0,0 +1,66 @@ + + + graphclust-wrappers + nspdk + + + + + + + + + + + + + + + + + + + + + + + + + + + (default: 1) ++ **-D** (default: 4) + + + ]]> + + + 10.1093/bioinformatics/bts224 + @inproceedings{costa2010fast, + title={Fast neighborhood subgraph pairwise distance kernel}, + author={Costa, Fabrizio and De Grave, Kurt}, + booktitle={Proceedings of the 26th International Conference on Machine Learning}, + pages={255--262}, + year={2010}, + organization={Omnipress} + } + + + diff -r 000000000000 -r 165fe96228be test-data/1.group.gspan.bz2 Binary file test-data/1.group.gspan.bz2 has changed diff -r 000000000000 -r 165fe96228be test-data/SVECTOR/data.svector Binary file test-data/SVECTOR/data.svector has changed diff -r 000000000000 -r 165fe96228be test-data/SVECTOR/data.svector.1.fast_cluster --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/SVECTOR/data.svector.1.fast_cluster Fri Dec 16 07:36:07 2016 -0500 @@ -0,0 +1,2 @@ +46 35 28 17 37 33 30 18 16 9 31 7 23 51 32 15 54 53 52 10 76 21 19 12 24 2 5 36 50 26 22 11 13 60 4 58 1 74 72 77 3 20 45 61 82 73 56 68 75 85 88 14 57 55 84 70 80 62 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RF00031_rep.0_X71973.1/730-791_62 ORIGHEAD RF00031_rep.0 +CCGGCACUCAUGACGGCCUGCCUGCAAACCUGCUGGUGGGGCAGACCCGAAAAUCCAGCGUG +>63 SEQ63#1#68#+ ORIGID RF00031_rep.1_U67171.1/375-442_63 ORIGHEAD RF00031_rep.1 +GACGCUUCAUGAUAGGAAGGACUGAAAAGUCUUGUGGACACCUGGUCUUUCCCUGAUGUUCUCGUGGC +>64 SEQ64#1#62#+ ORIGID RF00031_rep.2_S79854.1/1605-1666_64 ORIGHEAD RF00031_rep.2 +CACUGCUGAUGACGAACUAUCUCUAACUGGUCUUGACCACGAGCUAGUUCUGAAUUGCAGGG +>65 SEQ65#1#57#+ ORIGID RF00031_rep.3_X53463.1/847-903_65 ORIGHEAD RF00031_rep.3 +UUCACAGAAUGAUGGCACCUUCCUAAACCCUCAUGGGUGGUGUCUGAGAGGCGUGAA +>66 SEQ66#1#71#+ ORIGID RF00031_rep.4_AF195141.1/689-759_66 ORIGHEAD RF00031_rep.4 +GACUGACAUUAUGAAGGCCUGUACUGAAGACAGCAAGCUGUUAGUACAGACCAGAUGCUUUCUUGGCAGGC +>67 SEQ67#1#66#+ ORIGID RF00031_rep.5_AF093774.1/5851-5916_67 ORIGHEAD RF00031_rep.5 +GUGUGCGGAUGAUAACUACUGACGAAAGAGUCAUCGACCUCAGUUAGUGGUUGGAUGUAGUCACAU +>68 SEQ68#1#64#+ ORIGID RF00031_rep.6_BC003127.1/865-928_68 ORIGHEAD RF00031_rep.6 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ORIGID RF00618_rep.2_U62822.1/2-128_74 ORIGHEAD RF00618_rep.2 +ACCAUCCUUUUCUUGGGGUUGCGCUACUGUCCAAUGAGCGCAUAGUGAGGGCAGUACUGCUAACGCCUGAACAACACACCCGCAUCAACUAGAGCUUUUGCUUUAUUUUGGUGCAAUUUUUGGAAAA +>75 SEQ75#1#126#+ ORIGID RF00618_rep.3_AL389925.10/20736-20611_75 ORIGHEAD RF00618_rep.3 +ACCAUCCUUUUCUUGGGGUUGCACUACUGUCUAAUGAGUGCAUAAUGAGGGCAGUAUUGCUAACGCCUAUACAAUGCACCUGCAUCAACUAGAACUUUGCUUUACCUUGGUACAAUUUUUGGAAAA +>76 SEQ76#1#79#+ ORIGID RF00641_rep.0_AL132709.5/95865-95787_76 ORIGHEAD RF00641_rep.0 +GGUACUUGGAGAGAGGUGGUCCGUGGCGCGUUCGCUUUAUUUAUGGCGCACAUUACACGGUCGACCUCUUUGCAGUAUC +>77 SEQ77#1#77#+ ORIGID RF00641_rep.10_AADD01141100.1/2839-2915_77 ORIGHEAD RF00641_rep.10 +GGUACUCGGGGAGAGGUUACCCGAGCAACUUUGCAUCUGGACGACGAAUGUUGCUCGGUGAACCCCUUUUCGGUAUC +>78 SEQ78#1#80#+ ORIGID RF00641_rep.11_AC208187.2/25743-25822_78 ORIGHEAD RF00641_rep.11 +GGUAUUUGAAGAUGCGGUUGACCAUGGUGUGUACGCUUUAUUUGUGACGUAGGACACAUGGUCUACUUCUUCUCAAUAUC +>79 SEQ79#1#79#+ ORIGID RF00641_rep.12_AL132709.5/56006-55928_79 ORIGHEAD RF00641_rep.12 +GGUACUUGAAGGGAGAUCGACCGUGUUAUAUUCGCUUUAUUGACUUCGAAUAAUACAUGGUUGAUCUUUUCUCAGUAUC +>80 SEQ80#1#79#+ ORIGID RF00641_rep.13_AL132709.5/55165-55087_80 ORIGHEAD RF00641_rep.13 +GGUGCCUGAGGAGAGGUGGCCUGUGUUGCAUUCACAGAAAUCAUGACACACAAGACACGAGCGGCCUCUCUUCAGUAUC +>81 SEQ81#1#77#+ ORIGID RF00641_rep.1_AL132709.5/86350-86274_81 ORIGHEAD RF00641_rep.1 +GGUACUGGAGGAGAGGUUAUCUGUGUUUUUUCCCUUUAUUUAUGAUGAAAAAUAUGGUGCACUUCUAUUUGAGAAUC +>82 SEQ82#1#81#+ ORIGID RF00641_rep.2_AC208187.2/29806-29886_82 ORIGHEAD RF00641_rep.2 +GAUACUCGAAGGAGAGGUUGUCCGUGUUGUCUUCUCUUUAUUUAUGAUGAAACAUACACGGGAAACCUCUUUUUUAGUAUC +>83 SEQ83#1#79#+ ORIGID RF00641_rep.3_AADD01141098.1/2614-2692_83 ORIGHEAD RF00641_rep.3 +GCUACUUGAAGAGAGGUAAUCCUUCAUGCAUUUGCUUUACUUGCAAUGAUUAUACAAGGGCAGACUCUCUCUGGGGAGC +>84 SEQ84#1#79#+ ORIGID RF00641_rep.4_ABBA01048514.1/248685-248607_84 ORIGHEAD RF00641_rep.4 +GGUACUCGAAUGGAGGUUGUCCAUGGUGUGUUCAUUUUAUUUAUGAUGAGUAUUACAUGGCCAAUCUCCUUUCGGUACU +>85 SEQ85#1#79#+ ORIGID RF00641_rep.5_AL132709.5/73699-73621_85 ORIGHEAD RF00641_rep.5 +GGUGCUUAAAGAAUGGCUGUCCGUAGUAUGGUCUCUAUAUUUAUGAUGAUUAAUAUCGGACAACCAUUGUUUUAGUAUC +>86 SEQ86#1#79#+ ORIGID RF00641_rep.6_AADB02234051.1/94-172_86 ORIGHEAD RF00641_rep.6 +GGUACUUAAGGGGGAGGUGGGCUUUGAAUAAUAAGUUUAUUGACGUGGAAUAUACAAGGGCAAGCUCUCUGUGAGUAUC +>87 SEQ87#1#78#+ ORIGID RF00641_rep.7_AL132709.5/54880-54803_87 ORIGHEAD RF00641_rep.7 +GGUACCUGAAAUAGGUUGCCUGUGAGGUGUUCACUUUCUAUAUGAUGAAUAUUAUACAGUCAACCUCUUUCCGAUAUC +>88 SEQ88#1#81#+ ORIGID RF00641_rep.8_AL132709.5/61554-61474_88 ORIGHEAD RF00641_rep.8 +GGUACUGGUGGAGAGGUCUUCCAUGAUGCAUUCGAUUUAUUUUUUGACCAAUCCUACAUAGUGGACUCUUUUGAAAGCAUU +>89 SEQ89#1#80#+ ORIGID RF00641_rep.9_AL132709.5/98273-98194_89 ORIGHEAD RF00641_rep.9 +GGUACUUGGAGAGAUAGUAGACCGUAUAGCGUACGCUUUAUCUGUGACGUAUGUAACACGGUCCACUAACCCUCAGUAUC +>90 SEQ90#1#66#+ ORIGID RF00693_rep.0_AADD01093451.1/1636-1571_90 ORIGHEAD RF00693_rep.0 +AAUCUUAUGGAAACAUUUCUGCACACAAUAAAGAAACUAGUGUACAGAAAUGUUUACUUGUCUAUG +>91 SEQ91#1#69#+ ORIGID RF00693_rep.1_AL031669.28/23303-23371_91 ORIGHEAD RF00693_rep.1 +GGUCUAGUGGAAACAUUUCUGCACAACCAGAAUACUCAAACUAGCAUGAGGAAAGGCUUCUGUAACAGU +>92 SEQ92#1#69#+ ORIGID RF00693_rep.2_ABBA01075050.1/41249-41181_92 ORIGHEAD RF00693_rep.2 +UAUUUCGUGGAUGAUUUCUACACAGACUAGGCCAUAGAAACCAGUGCGUAGAAAUGCUUCUGUUACAUG diff -r 000000000000 -r 165fe96228be test-data/data.names --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/data.names Fri Dec 16 07:36:07 2016 -0500 @@ -0,0 +1,92 @@ +1 SEQ1#1#120#+ ORIGID RF00001_rep.0_AL096764.11/46123-46004_1 ORIGHEAD RF00001_rep.0 +2 SEQ2#1#118#+ ORIGID RF00001_rep.1_U89919.1/939-1056_2 ORIGHEAD RF00001_rep.1 +3 SEQ3#1#104#+ ORIGID RF00001_rep.2_AJ508600.1/161-58_3 ORIGHEAD RF00001_rep.2 +4 SEQ4#1#73#+ ORIGID RF00005_rep.0_M15347.1/1040-968_4 ORIGHEAD RF00005_rep.0 +5 SEQ5#1#72#+ ORIGID RF00005_rep.10_X58792.1/174-245_5 ORIGHEAD RF00005_rep.10 +6 SEQ6#1#66#+ ORIGID RF00005_rep.11_AF346992.1/15890-15955_6 ORIGHEAD RF00005_rep.11 +7 SEQ7#1#83#+ ORIGID RF00005_rep.12_AC108081.2/59868-59786_7 ORIGHEAD RF00005_rep.12 +8 SEQ8#1#70#+ ORIGID RF00005_rep.13_AC067849.6/4771-4840_8 ORIGHEAD RF00005_rep.13 +9 SEQ9#1#73#+ ORIGID RF00005_rep.14_AL021808.2/65570-65498_9 ORIGHEAD RF00005_rep.14 +10 SEQ10#1#73#+ ORIGID RF00005_rep.15_AC008443.10/42590-42518_10 ORIGHEAD RF00005_rep.15 +11 SEQ11#1#82#+ ORIGID RF00005_rep.16_AL133551.13/12355-12436_11 ORIGHEAD RF00005_rep.16 +12 SEQ12#1#82#+ ORIGID RF00005_rep.17_AL021918.1/54817-54736_12 ORIGHEAD RF00005_rep.17 +13 SEQ13#1#82#+ ORIGID RF00005_rep.18_AL021918.1/81116-81197_13 ORIGHEAD RF00005_rep.18 +14 SEQ14#1#73#+ ORIGID RF00005_rep.19_AF134583.1/1816-1744_14 ORIGHEAD RF00005_rep.19 +15 SEQ15#1#73#+ ORIGID RF00005_rep.1_AC005329.1/7043-6971_15 ORIGHEAD RF00005_rep.1 +16 SEQ16#1#72#+ ORIGID RF00005_rep.20_AL671879.2/100356-100285_16 ORIGHEAD RF00005_rep.20 +17 SEQ17#1#71#+ ORIGID RF00005_rep.21_AL355149.13/15278-15208_17 ORIGHEAD RF00005_rep.21 +18 SEQ18#1#72#+ ORIGID 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