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Commit message:
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/LocARNAGraphClust commit f971832d2b34a182314e5201ea6895dd207c5923 |
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modified:
locarna_best_subtree.xml |
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| diff -r 606440a3852d -r 51261dff08a5 locarna_best_subtree.xml --- a/locarna_best_subtree.xml Mon Feb 27 12:02:38 2017 -0500 +++ b/locarna_best_subtree.xml Mon Mar 13 18:02:55 2017 -0400 |
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| b'@@ -1,6 +1,6 @@\n <tool id="locarna_best_subtree" name="locarna_graphclust" version="0.1.0" >\n <requirements>\n- <requirement type="package" version="0.1.9">graphclust-wrappers</requirement>\n+ <requirement type="package" version="0.1.10">graphclust-wrappers</requirement>\n <requirement type="package" version=\'1.8.10\'>locarna</requirement>\n <requirement type="package" version=\'2.1\'>rnaz</requirement>\n <requirement type="package" version=\'0.07\'>perl-math-round</requirement>\n@@ -11,9 +11,16 @@\n <command>\n <![CDATA[\n \n- \'locARNAGraphClust.pl\' \'$center_fa_file\' \'$tree_file\' \'$tree_matrix\' \'$data_map\' $allow_overlap\n+ locARNAGraphClust.pl \n+ \'$center_fa_file\'\n+ \'$tree_file\'\n+ \'$tree_matrix\'\n+ \'$data_map\'\n+ $allow_overlap\n+ $free_endgaps\n+\n #if str($param_type.param_type_selector) == "gclust"\n- $param_type.p\n+ $param_type.p\n $param_type.max_diff_am\n $param_type.max_diff\n $param_type.tau\n@@ -34,76 +41,74 @@\n <param type="data" name="data_map" label="data_map" format="txt" help="text format" />\n <param name="allow_overlap" type="boolean" truevalue="1" falsevalue="0" label="Allow overlap in subtrees" help="otherwise ignore subtree if it contains overlapping sequences"/>\n \n- <conditional name="param_type">\n- <param name="param_type_selector" type="select" label="Choose the type of parameters">\n- <option value="locarna">LocARNA defaults</option>\n- <option value="gclust" selected="True">GrapClust defaults(changeable)</option>\n+ <param name="free_endgaps" type="select" label="Free endgaps"\n+ help="Specify whether gaps at the ends (all, 5\', or 3\' ends)\n+ of the sequences should be penalized or allowed for free.">\n+ <option value="0">No free endgaps</option>\n+ <option value="--free-endgaps">Free endgaps</option>\n+ <option value="--free-endgaps-5">Free endgaps, only 5\'</option>\n+ <option value="--free-endgaps-3">Free endgaps, only 3\'</option>\n </param>\n- <when value="gclust">\n-\n- <param name="p" type="float" value="0.001" size="5" label="minimal probability" help="-p"/>\n- <param name="max_diff_am" type="integer" value="50" size="5" label=" maximal difference for sizes of matched arcs" help="--max-diff-am"/>\n- <param argument="tau" type="integer" value="50" min="0" max="200" label="Sequence contribution at structure match in percent"/>\n- <param name="max_diff" type="integer" value="100" size="5" label="maximal difference for alignment traces" help="--max-diff"/>\n- <param name="plfold_minlen" type="integer" value="210" size="5" label="Minimal length of a sequences for which RNAplfold is used" />\n-\n- <param name="struct_weight" argument="struct-weight"\n- label="Structure weight" type="integer"\n- value="180" min="0" max="800" />\n- <param name="indel_opening" argument="indel-opening"\n- label="Indel opening score" type="integer"\n- value="-400" max="0" min="-1500" />\n- <param argument="indel" label="Indel score" type="integer"\n- value="-200" min="-1000" max="0" />\n-\n- <param name="alifold_consensus_dp"\n- type="boolean" checked="True"\n- truevalue="--alifold-consensus-dp" falsevalue=" "\n- label="Compute consensus dot plot by alifold" />\n-\n- <param name="plfold_span"\n- type="integer" value="150" min="-1" max="400"\n- label="Maximum basepair span by RNAplfold (local folding); -1 for global folding" />\n-\n- <param name="plfold_winsize"\n+ <conditional name="param_type">\n+ <param name="param_type_selector" type="select" label="Choose the type of parameters">\n+ <option value="locarna">LocARNA defaults</option>\n+ <option value="gclust" selected="True">GrapClust defaults(c'..b' {4},\n- pages = {e65},\n- issn = {1553-7358},\n- issn = {1553-734X},\n- pmid = {17432929},\n- doi = {10.1371/journal.pcbi.0030065},\n- user = {will},\n- abstract = {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- </citation>\n- <citation type="bibtex">@Article{Smith:Heyne:Richter:Freib_RNA_Tools:NAR2010,\n- author = {Smith, Cameron and Heyne, Steffen and Richter, Andreas S.\n- and Will, Sebastian and Backofen, Rolf},\n- title = {Freiburg {RNA} {Tools}: a web server integrating {IntaRNA},\n- {ExpaRNA} and {LocARNA}},\n- journal = NAR,\n- year = {2010},\n- volume = {38 Suppl},\n- number = {},\n- pages = {W373-7},\n- user = {arichter},\n- pmid = {20444875},\n- doi = {10.1093/nar/gkq316},\n- issn = {0305-1048},\n- issn = {1362-4962},\n- abstract = {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- </citation>\n+ <citation type="doi">10.1261/rna.029041.111</citation>\n+ <citation type="doi">10.1371/journal.pcbi.0030065</citation>\n+ <citation type="doi">10.1093/nar/gkq316</citation>\n </citations>\n </tool>\n' |