| Next changeset 1:c6c4a7adb099 (2017-01-21) |
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Commit message:
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/LocARNAGraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053 |
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added:
locarna_best_subtree.xml test-data/1.1.center.fa test-data/1.1.matrix.tree test-data/1.1.tree test-data/best_subtree.aln test-data/data.map |
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| diff -r 000000000000 -r 15bd4fb05e5c locarna_best_subtree.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/locarna_best_subtree.xml Fri Dec 16 07:35:29 2016 -0500 |
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| b'@@ -0,0 +1,190 @@\n+<tool id="locarna_best_subtree" name="locarna_best_subtree" version="0.1.0" >\n+\t<requirements>\n+\t\t<requirement type="package" version="0.1">graphclust-wrappers</requirement>\n+\t\t<requirement type="package" version=\'1.8.10\'>locarna</requirement>\n+\t\t<requirement type="package" version=\'2.1\'>rnaz</requirement>\n+\t\t<requirement type="package" version=\'0.07\'>perl-math-round</requirement>\n+\t</requirements>\n+\t<stdio>\n+\t\t<exit_code range="1:" />\n+\t</stdio>\n+\t<command>\n+\t\t<![CDATA[\n+\n+\t\t \'locARNAGraphClust.pl\' \'$center_fa_file\' \'$tree_file\' \'$tree_matrix\' $p $max_diff_am $tau $max_diff \'\' \'$data_map\' $plfold_minlen\n+ ]]>\n+\t</command>\n+\t<inputs>\n+\t\t<param type="data" name="center_fa_file" label="centers" format="fa, fasta" help="fasta format" />\n+\t\t<param type="data" name="tree_file" label="trees" format="text" help="text format" />\n+\t\t<param type="data" name="tree_matrix" label="tree_matrix" format="text" help="text format" />\n+\t\t<param type="data" name="data_map" label="data_map" format="txt" help="text format" />\n+\t\t<param name="p" type="float" value="0.001" size="5" label="minimal probability" help="-p"/>\n+\t\t<param name="max_diff_am" type="integer" value="50" size="5" label=" maximal difference for sizes of matched arcs" help="--max-diff-am"/>\n+\t\t<param name="tau" type="integer" value="50" size="5" label="Tau factor in percent" help="--tau"/>\n+\t\t<param name="max_diff" type="integer" value="100" size="5" label="maximal difference for alignment traces" help="--max-diff"/>\n+\t\t<param name="plfold_minlen" type="integer" value="210" size="5" label="Minimal length of a sequences for which RNAplfold is used" />\n+\t</inputs>\n+\t<outputs>\n+\n+\t\t<data name="model_tree_stk" format="stockholm" label="model.tree.stk" from_work_dir="MODEL/best_subtree.aln" />\n+\t</outputs>\n+\t<tests>\n+\t\t<test>\n+\t\t\t<param name="tree_file" value="1.1.tree"/>\n+\t\t\t<param name="center_fa_file" value="1.1.center.fa"/>\n+\t\t\t<param name="data_map" value="data.map"/>\n+\t\t\t<param name="tree_matrix" value="1.1.matrix.tree"/>\n+\t\t\t<param name="p" value="0.001"/>\n+\t\t\t<param name="max-diff-am" value="50"/>\n+\t\t\t<param name="tau" value="50"/>\n+\t\t\t<param name="max-diff-am" value="100"/>\n+\t\t\t<output name="model_tree_stk" file="best_subtree.aln"/>\n+\t\t</test>\n+\t</tests>\n+\t<help>\n+\t\t<![CDATA[\n+**What it does**\n+\n+MLocARNA computes a multiple sequence-structure alignment of RNA sequences.\n+It uses *treefile* - file with guide tree in NEWICK format. The given tree is used as guide tree for the progressive alignment.\n+This saves the calculation of pairwise all-vs-all similarities and construction of the guide tree.\n+\n+\n+\n+]]>\n+\t</help>\n+\t<citations>\n+\t\t<citation type="bibtex">@inproceedings{costa2010fast,\n+ title={Fast neighborhood subgraph pairwise distance kernel},\n+ author={Costa, Fabrizio and De Grave, Kurt},\n+ booktitle={Proceedings of the 26th International Conference on Machine Learning},\n+ pages={255--262},\n+ year={2010},\n+ organization={Omnipress}\n+ }\n+ </citation>\n+\t\t\t<citation type="bibtex">@Article{Will_Joshi_Hofacker-LocAR_Accur_bound-2012,\n+ author =\t {Will, Sebastian and Joshi, Tejal and Hofacker, Ivo L. and\n+ Stadler, Peter F. and Backofen, Rolf},\n+ title =\t {{LocARNA}-{P}: {Accurate} boundary prediction and improved\n+ detection of structural {RNAs}},\n+ journal =\t {RNA},\n+ year =\t {2012},\n+ volume =\t {18},\n+ number =\t {5},\n+ pages =\t {900-14},\n+ user =\t {will},\n+ pmid =\t {22450757},\n+ doi = \t {10.1261/rna.029041.111},\n+ issn = \t {1469-9001},\n+ issn = \t {1355-8382},\n+ abstract =\t {Current genomic screens for noncoding RNAs (ncRNAs) predict\n+ a large number of genomic regions containing potential\n+ structural ncRNAs. The analysis of these data requires\n+ highly accurate prediction of ncRNA boundaries and\n+ discrimination of promising candidate ncRNAs from weak\n+ prediction'..b'+ title =\t {Inferring Non-Coding {RNA} Families and Classes by Means of\n+ Genome-Scale Structure-Based Clustering},\n+ journal =\t {PLoS Comput Biol},\n+ year =\t 2007,\n+ volume = {3},\n+ number = {4},\n+ pages = {e65},\n+ issn = {1553-7358},\n+ issn = {1553-734X},\n+ pmid = {17432929},\n+ doi = {10.1371/journal.pcbi.0030065},\n+ user =\t {will},\n+ abstract =\t {The RFAM database defines families of ncRNAs by means of\n+ sequence similarities that are sufficientto establish\n+ homology. In some cases, such as microRNAs, box H/ACA\n+ snoRNAs, functional commonalities define classes of RNAs\n+ that are characterized by structural similarities, and\n+ typically consist ofmultiple RNA families. Recent advances\n+ in high-throughput transcriptomics and comparative genomics\n+ have produced very large sets of putative non-coding RNAs\n+ and regulatory RNA signals. For many ofthem, evidence for\n+ stabilizing selection acting on their secondary structures\n+ has been derived, and at least approximate models of their\n+ structures have been computed. The overwhelming majority of\n+ these hypo-thetical RNAs cannot be assigned to established\n+ families or classes. We present here a structure-based\n+ clustering approach that is capable of extracting putative\n+ RNA classesfrom genome-wide surveys for structured RNAs. The\n+ LocARNA tool implements a novel variant of theSankoff\n+ algorithm that is sufficiently fast to deal with several\n+ thousand candidate sequences. The method is also robust\n+ against false positive predictions, i.e., a contamination of\n+ the input data with unstructured ornon-conserved\n+ sequences. We have successfully tested the LocARNA-based\n+ clustering approach on the sequences of the\n+ RFAM-seedalignments. Furthermore, we have applied it to a\n+ previously published set of 3332 predicted structured\n+ elements in the Ciona intestinalis genomes (Missal et al.,\n+ Bioinformatics 21(S2), i77-i78). In addition torecovering\n+ e.g. tRNAs as a structure-based class, the method identifies\n+ several RNA families, including microRNA and snoRNA\n+ candidates, and suggests several novel classes of ncRNAs for\n+ which to-date norepresentative has been experimentally\n+ characterized.}\n+}\n+\n+\t\t\t\t\t</citation>\n+\t\t\t\t\t<citation type="bibtex">@Article{Smith:Heyne:Richter:Freib_RNA_Tools:NAR2010,\n+ author =\t {Smith, Cameron and Heyne, Steffen and Richter, Andreas S.\n+ and Will, Sebastian and Backofen, Rolf},\n+ title =\t {Freiburg {RNA} {Tools}: a web server integrating {IntaRNA},\n+ {ExpaRNA} and {LocARNA}},\n+ journal =\t NAR,\n+ year =\t {2010},\n+ volume =\t {38 Suppl},\n+ number =\t {},\n+ pages =\t {W373-7},\n+ user =\t {arichter},\n+ pmid =\t {20444875},\n+ doi = \t {10.1093/nar/gkq316},\n+ issn = \t {0305-1048},\n+ issn =\t {1362-4962},\n+ abstract =\t {The Freiburg RNA tools web server integrates three tools\n+ for the advanced analysis of RNA in a common web-based user\n+ interface. The tools IntaRNA, ExpaRNA and LocARNA support\n+ the prediction of RNA-RNA interaction, exact RNA matching\n+ and alignment of RNA, respectively. The Freiburg RNA tools\n+ web server and the software packages of the stand-alone\n+ tools are freely accessible at\n+ http://rna.informatik.uni-freiburg.de.}\n+}\n+\t\t\t\t\t\t</citation>\n+\t</citations>\n+</tool>\n' |
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| diff -r 000000000000 -r 15bd4fb05e5c test-data/1.1.center.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/1.1.center.fa Fri Dec 16 07:35:29 2016 -0500 |
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| @@ -0,0 +1,40 @@ +>7 SEQ7#1#83#+ ORIGID RF00005_rep.12_AC108081.2/59868-59786_7 ORIGHEAD RF00005_rep.12 +GUCAGGAUGGCCGAGCGGUCUAAGGCGCUGCGUUCAGGUCGCAGUCUCCCCUGGAGGCGUGGGUUCGAAUCCCACUUCUGACA +>9 SEQ9#1#73#+ ORIGID RF00005_rep.14_AL021808.2/65570-65498_9 ORIGHEAD RF00005_rep.14 +GCUUCUGUAGUGUAGUGGUUAUCACGUUCGCCUCACACGCGAAAGGUCCCCGGUUCGAAACCGGGCAGAAGCA +>10 SEQ10#1#73#+ ORIGID RF00005_rep.15_AC008443.10/42590-42518_10 ORIGHEAD RF00005_rep.15 +GCCCGGCUAGCUCAGUCGGUAGAGCAUGAGACUCUUAAUCUCAGGGUCGUGGGUUCGAGCCCCACGUUGGGCG +>15 SEQ15#1#73#+ ORIGID RF00005_rep.1_AC005329.1/7043-6971_15 ORIGHEAD RF00005_rep.1 +GCCGAAAUAGCUCAGUUGGGAGAGCGUUAGACUGAAGAUCUAAAGGUCCCUGGUUCGAUCCCGGGUUUCGGCA +>16 SEQ16#1#72#+ ORIGID RF00005_rep.20_AL671879.2/100356-100285_16 ORIGHEAD RF00005_rep.20 +GGGGAUGUAGCUCAGUGGUAGAGCGCAUGCUUCGCAUGUAUGAGGCCCCGGGUUCGAUCCCCGGCAUCUCCA +>17 SEQ17#1#71#+ ORIGID RF00005_rep.21_AL355149.13/15278-15208_17 ORIGHEAD RF00005_rep.21 +GCAUUGGUGGUUCAGUGGUAGAAUUCUCGCCUCCCACGCGGGAGACCCGGGUUCAAUUCCCGGCCAAUGCA +>18 SEQ18#1#72#+ ORIGID RF00005_rep.22_AL590385.23/26487-26416_18 ORIGHEAD RF00005_rep.22 +GCGUUGGUGGUAUAGUGGUGAGCAUAGCUGCCUUCCAAGCAGUUGACCCGGGUUCGAUUCCCGGCCAACGCA +>23 SEQ23#1#74#+ ORIGID RF00005_rep.27_AL352978.6/119697-119770_23 ORIGHEAD RF00005_rep.27 +GGCCGGUUAGCUCAGUUGGUUAGAGCGUGGUGCUAAUAACGCCAAGGUCGCGGGUUCGAUCCCCGUACGGGCCA +>28 SEQ28#1#71#+ ORIGID RF00005_rep.31_AC092686.3/29631-29561_28 ORIGHEAD RF00005_rep.31 +GCAUUGGUGGUUCAGUGGUAGAAUUCUCGCCUGCCACGCGGGAGGCCCGGGUUCGAUUCCCGGCCAAUGCA +>30 SEQ30#1#72#+ ORIGID RF00005_rep.33_AC018638.5/4694-4623_30 ORIGHEAD RF00005_rep.33 +GGCUCGUUGGUCUAGGGGUAUGAUUCUCGCUUAGGGUGCGAGAGGUCCCGGGUUCAAAUCCCGGACGAGCCC +>31 SEQ31#1#73#+ ORIGID RF00005_rep.34_AC008443.10/43006-42934_31 ORIGHEAD RF00005_rep.34 +GUUUCCGUAGUGUAGUGGUUAUCACGUUCGCCUCACACGCGAAAGGUCCCCGGUUCGAAACCGGGCGGAAACA +>32 SEQ32#1#73#+ ORIGID RF00005_rep.35_AC005783.1/27398-27326_32 ORIGHEAD RF00005_rep.35 +GUUUCCGUAGUGUAGCGGUUAUCACAUUCGCCUCACACGCGAAAGGUCCCCGGUUCGAUCCCGGGCGGAAACA +>33 SEQ33#1#72#+ ORIGID RF00005_rep.36_AC007298.17/145366-145295_33 ORIGHEAD RF00005_rep.36 +UCCUCGUUAGUAUAGUGGUGAGUAUCCCCGCCUGUCACGCGGGAGACCGGGGUUCGAUUCCCCGACGGGGAG +>35 SEQ35#1#72#+ ORIGID RF00005_rep.38_J00309.1/356-427_35 ORIGHEAD RF00005_rep.38 +UCCCUGGUGGUCUAGUGGCUAGGAUUCGGCGCUUUCACCGCCGCGCCCCGGGUUCGAUUCCCGGCCAGGAAU +>37 SEQ37#1#82#+ ORIGID RF00005_rep.3_Z54587.1/126-45_37 ORIGHEAD RF00005_rep.3 +GGUAGCGUGGCCGAGCGGUCUAAGGCGCUGGAUUUAGGCUCCAGUCUCUUCGGAGGCGUGGGUUCGAAUCCCACCGCUGCCA +>46 SEQ46#1#72#+ ORIGID RF00005_rep.5_AL590385.23/26129-26058_46 ORIGHEAD RF00005_rep.5 +UCCCUGGUGGUCUAGUGGUUAGGAUUCGGCGCUCUCACCGCCGCGGCCCGGGUUCGAUUCCCGGUCAGGGAA +>51 SEQ51#1#88#+ ORIGID RF00006_rep.0_AF045145.1/1-88_51 ORIGHEAD RF00006_rep.0 +GGCUGGCUUUAGCUCAGCGGUUACUUCGCGUGUCAUCAAACCACCUCUCUGGGUUGUUCGAGACCCGCGGGCGCUCUCCAGCCCUCUU +>52 SEQ52#1#101#+ ORIGID RF00006_rep.1_AC005219.1/49914-50014_52 ORIGHEAD RF00006_rep.1 +GGGUCGGAGUUAGCUCAAGCGGUUACCUCCUCAUGCCGGACUUUCUAUCUGUCCAUCUCUGUGCUGGGGUUCGAGACCCGCGGGUGCUUACUGACCCUUUU +>53 SEQ53#1#98#+ ORIGID RF00006_rep.2_AF045143.1/1-98_53 ORIGHEAD RF00006_rep.2 +GGCUGGCUUUAGCUCAGCGGUUACUUCGACAGUUCUUUAAUUGAAACAAGCAACCUGUCUGGGUUGUUCGAGACCCGCGGGCGCUCUCCAGUCCUUUU +>54 SEQ54#1#88#+ ORIGID RF00006_rep.3_AF045144.1/1-88_54 ORIGHEAD RF00006_rep.3 +GGCUGGCUUUAGCUCAGCGGUUACUUCGAGUACAUUGUAACCACCUCUCUGGGUGGUUCGAGACCCGCGGGUGCUUUCCAGCUCUUUU |
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| diff -r 000000000000 -r 15bd4fb05e5c test-data/1.1.matrix.tree --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/1.1.matrix.tree Fri Dec 16 07:35:29 2016 -0500 |
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| diff -r 000000000000 -r 15bd4fb05e5c test-data/1.1.tree --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/1.1.tree Fri Dec 16 07:35:29 2016 -0500 |
| b |
| @@ -0,0 +1,1 @@ +(((((54:0.133216,(53:0.115952,51:0.115952):0.0172647):0.0413516,52:0.174568):0.0233911,(37:0.150476,7:0.150476):0.047483):0.00361419,(((23:0.184455,16:0.184455):0.0038835,10:0.188338):0.00251517,15:0.190853):0.01072):0.00340405,((((46:0.099691,35:0.099691):0.0793888,((28:0.066725,17:0.066725):0.105711,18:0.172436):0.00664407):0.0153606,30:0.19444):0.00190942,(33:0.187757,((32:0,31:0):0.066541,9:0.066541):0.121216):0.00859264):0.00862737):0 |
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| diff -r 000000000000 -r 15bd4fb05e5c test-data/best_subtree.aln --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/best_subtree.aln Fri Dec 16 07:35:29 2016 -0500 |
| b |
| @@ -0,0 +1,8 @@ +CLUSTAL W --- LocARNA 1.8.10 + +18 GCGUUGGUGGUAUAGUGGUGAGCAUAGCUGCCUUCCAAGCAGUUGA-CCCGGGUUCGAUUCCCGGCCAACGCA +17 GCAUUGGUGGUUCAGUGGU-AGAAUUCUCGCCUCCCACGCGGGAGA-CCCGGGUUCAAUUCCCGGCCAAUGCA +28 GCAUUGGUGGUUCAGUGGU-AGAAUUCUCGCCUGCCACGCGGGAGG-CCCGGGUUCGAUUCCCGGCCAAUGCA +46 UCCCUGGUGGUCUAGUGGUUAGGAUUCGGCGCUCUCACCGCCGCGG-CCCGGGUUCGAUUCCCGGUCAGGGAA +35 UCCCUGGUGGUCUAGUGGCUAGGAUUCGGCGCUUUCACCGCCGCGC-CCCGGGUUCGAUUCCCGGCCAGGAAU +30 GGCUCGUUGGUCUAGGGGU-AUGAUUCUCGCUUAGGGUGCGAGAGGUCCCGGGUUCAAAUCCCGGACGAGCCC |
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| diff -r 000000000000 -r 15bd4fb05e5c test-data/data.map --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/data.map Fri Dec 16 07:35:29 2016 -0500 |
| b |
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