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Commit message:
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/LocARNAGraphClust commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 |
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modified:
locarna_best_subtree.xml |
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| diff -r 15bd4fb05e5c -r c6c4a7adb099 locarna_best_subtree.xml --- a/locarna_best_subtree.xml Fri Dec 16 07:35:29 2016 -0500 +++ b/locarna_best_subtree.xml Sat Jan 21 17:39:36 2017 -0500 |
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| b'@@ -1,49 +1,110 @@\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+ <requirements>\n+ <requirement type="package" version="0.1.7">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+ </requirements>\n+ <stdio>\n+ <exit_code range="1:" />\n+ </stdio>\n+ <command>\n+ <![CDATA[\n \n-\t\t \'locARNAGraphClust.pl\' \'$center_fa_file\' \'$tree_file\' \'$tree_matrix\' $p $max_diff_am $tau $max_diff \'\' \'$data_map\' $plfold_minlen\n+ \'locARNAGraphClust.pl\' \'$center_fa_file\' \'$tree_file\' \'$tree_matrix\' \'$data_map\'\n+ #if str($param_type.param_type_selector) == "gclust"\n+ $param_type.p\n+ $param_type.max_diff_am\n+ $param_type.max_diff\n+ $param_type.tau\n+ $param_type.plfold_minlen\n+ $param_type.struct_weight\n+ $param_type.indel_opening\n+ $param_type.indel\n+ $param_type.alifold_consensus_dp\n+ $param_type.plfold_span\n+ $param_type.plfold_winsize\n+ #end if\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+ </command>\n+ <inputs>\n+ <param type="data" name="center_fa_file" label="centers" format="fa, fasta" help="fasta format" />\n+ <param type="data" name="tree_file" label="trees" format="text" help="text format" />\n+ <param type="data" name="tree_matrix" label="tree_matrix" format="text" help="text format" />\n+ <param type="data" name="data_map" label="data_map" format="txt" help="text format" />\n+\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>\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 '..b'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+ journal = {RNA},\n+ year = {2012},\n+ volume = {18},\n+ number = {5},\n+ pages = {900-14},\n+ user = {will},\n+ pmid = {22450757},\n+ doi = {10.1261/rna.029041.111},\n+ issn = {1469-9001},\n+ issn = {1355-8382},\n+ abstract = {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@@ -110,14 +171,14 @@\n for refining screens for structural ncRNA, at\n http://www.bioinf.uni-freiburg.de/Supplements/LocARNA-P/.}\n }\n-\t\t\t\t</citation>\n-\t\t\t\t<citation type="bibtex">@Article{Will:etal:_infer_non_codin_rna_famil:PLOS2007,\n- author =\t {Sebastian Will and Kristin Reiche and Ivo L. Hofacker and\n+ </citation>\n+ <citation type="bibtex">@Article{Will:etal:_infer_non_codin_rna_famil:PLOS2007,\n+ author = {Sebastian Will and Kristin Reiche and Ivo L. Hofacker and\n Peter F. Stadler and Rolf Backofen},\n- title =\t {Inferring Non-Coding {RNA} Families and Classes by Means of\n+ title = {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+ journal = {PLoS Comput Biol},\n+ year = 2007,\n volume = {3},\n number = {4},\n pages = {e65},\n@@ -125,8 +186,8 @@\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+ 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@@ -160,23 +221,23 @@\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+ </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 =\t {Freiburg {RNA} {Tools}: a web server integrating {IntaRNA},\n+ title = {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+ 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@@ -185,6 +246,6 @@\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+ </citation>\n+ </citations>\n </tool>\n' |