Mercurial > repos > rnateam > graphclust_mlocarna
changeset 1:c6c4a7adb099 draft
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/LocARNAGraphClust commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
author | rnateam |
---|---|
date | Sat, 21 Jan 2017 17:39:36 -0500 |
parents | 15bd4fb05e5c |
children | 5970f6f2a36b |
files | locarna_best_subtree.xml |
diffstat | 1 files changed, 145 insertions(+), 84 deletions(-) [+] |
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--- 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 @@ -1,49 +1,110 @@ <tool id="locarna_best_subtree" name="locarna_best_subtree" version="0.1.0" > - <requirements> - <requirement type="package" version="0.1">graphclust-wrappers</requirement> - <requirement type="package" version='1.8.10'>locarna</requirement> - <requirement type="package" version='2.1'>rnaz</requirement> - <requirement type="package" version='0.07'>perl-math-round</requirement> - </requirements> - <stdio> - <exit_code range="1:" /> - </stdio> - <command> - <![CDATA[ + <requirements> + <requirement type="package" version="0.1.7">graphclust-wrappers</requirement> + <requirement type="package" version='1.8.10'>locarna</requirement> + <requirement type="package" version='2.1'>rnaz</requirement> + <requirement type="package" version='0.07'>perl-math-round</requirement> + </requirements> + <stdio> + <exit_code range="1:" /> + </stdio> + <command> + <![CDATA[ - 'locARNAGraphClust.pl' '$center_fa_file' '$tree_file' '$tree_matrix' $p $max_diff_am $tau $max_diff '' '$data_map' $plfold_minlen + 'locARNAGraphClust.pl' '$center_fa_file' '$tree_file' '$tree_matrix' '$data_map' + #if str($param_type.param_type_selector) == "gclust" + $param_type.p + $param_type.max_diff_am + $param_type.max_diff + $param_type.tau + $param_type.plfold_minlen + $param_type.struct_weight + $param_type.indel_opening + $param_type.indel + $param_type.alifold_consensus_dp + $param_type.plfold_span + $param_type.plfold_winsize + #end if ]]> - </command> - <inputs> - <param type="data" name="center_fa_file" label="centers" format="fa, fasta" help="fasta format" /> - <param type="data" name="tree_file" label="trees" format="text" help="text format" /> - <param type="data" name="tree_matrix" label="tree_matrix" format="text" help="text format" /> - <param type="data" name="data_map" label="data_map" format="txt" help="text format" /> - <param name="p" type="float" value="0.001" size="5" label="minimal probability" help="-p"/> - <param name="max_diff_am" type="integer" value="50" size="5" label=" maximal difference for sizes of matched arcs" help="--max-diff-am"/> - <param name="tau" type="integer" value="50" size="5" label="Tau factor in percent" help="--tau"/> - <param name="max_diff" type="integer" value="100" size="5" label="maximal difference for alignment traces" help="--max-diff"/> - <param name="plfold_minlen" type="integer" value="210" size="5" label="Minimal length of a sequences for which RNAplfold is used" /> - </inputs> - <outputs> + </command> + <inputs> + <param type="data" name="center_fa_file" label="centers" format="fa, fasta" help="fasta format" /> + <param type="data" name="tree_file" label="trees" format="text" help="text format" /> + <param type="data" name="tree_matrix" label="tree_matrix" format="text" help="text format" /> + <param type="data" name="data_map" label="data_map" format="txt" help="text format" /> + + + <conditional name="param_type"> + <param name="param_type_selector" type="select" label="Choose the type of parameters"> + <option value="locarna">LocARNA defaults</option> + <option value="gclust" selected="True">GrapClust defaults(changeable)</option> + </param> + <when value="gclust"> + + <param name="p" type="float" value="0.001" size="5" label="minimal probability" help="-p"/> + <param name="max_diff_am" type="integer" value="50" size="5" label=" maximal difference for sizes of matched arcs" help="--max-diff-am"/> + <param argument="tau" type="integer" value="50" min="0" max="200" label="Sequence contribution at structure match in percent"/> + <param name="max_diff" type="integer" value="100" size="5" label="maximal difference for alignment traces" help="--max-diff"/> + <param name="plfold_minlen" type="integer" value="210" size="5" label="Minimal length of a sequences for which RNAplfold is used" /> + + <param name="struct_weight" argument="struct-weight" + label="Structure weight" type="integer" + value="180" min="0" max="800" /> + <param name="indel_opening" argument="indel-opening" + label="Indel opening score" type="integer" + value="-400" max="0" min="-1500" /> + <param argument="indel" label="Indel score" type="integer" + value="-200" min="-1000" max="0" /> + + <param name="alifold_consensus_dp" + type="boolean" checked="True" + truevalue="--alifold-consensus-dp" falsevalue=" " + label="Compute consensus dot plot by alifold" /> + + <param name="plfold_span" + type="integer" value="150" min="-1" max="400" + label="Maximum basepair span by RNAplfold (local folding); -1 for global folding" /> - <data name="model_tree_stk" format="stockholm" label="model.tree.stk" from_work_dir="MODEL/best_subtree.aln" /> - </outputs> - <tests> - <test> - <param name="tree_file" value="1.1.tree"/> - <param name="center_fa_file" value="1.1.center.fa"/> - <param name="data_map" value="data.map"/> - <param name="tree_matrix" value="1.1.matrix.tree"/> - <param name="p" value="0.001"/> - <param name="max-diff-am" value="50"/> - <param name="tau" value="50"/> - <param name="max-diff-am" value="100"/> - <output name="model_tree_stk" file="best_subtree.aln"/> - </test> - </tests> - <help> - <![CDATA[ + <param name="plfold_winsize" + type="integer" value="300" min="-1" max="800" + label="Window size for local folding" /> + + + </when> + <when value="locarna"> + </when> +</conditional> + + </inputs> + <outputs> + + <data name="model_tree_stk" format="stockholm" label="model.tree.stk" from_work_dir="MODEL/best_subtree.aln" /> + </outputs> + <tests> + <test> + <param name="tree_file" value="1.1.tree"/> + <param name="center_fa_file" value="1.1.center.fa"/> + <param name="data_map" value="data.map"/> + <param name="tree_matrix" value="1.1.matrix.tree"/> + <conditional name="param_type"> + <param name="iteration_num_selector" value="gclust"/> + <param name="p" value="0.001"/> + <param name="max_diff_am" value="50"/> + <param name="tau" value="50"/> + <param name="max_diff" value="100"/> + <param name="plfold_minlen" value="210"/> + <param name="struct_weight" value="180"/> + <param name="indel_opening" value="-400"/> + <param name="indel" value="-200"/> + <param name="alifold_consensus_dp" value="--alifold-consensus-dp"/> + <param name="plfold_span" value="150"/> + <param name="plfold_winsize" value="300"/> + </conditional> + <output name="model_tree_stk" file="best_subtree.aln"/> + </test> + </tests> + <help> + <![CDATA[ **What it does** MLocARNA computes a multiple sequence-structure alignment of RNA sequences. @@ -53,9 +114,9 @@ ]]> - </help> - <citations> - <citation type="bibtex">@inproceedings{costa2010fast, + </help> + <citations> + <citation type="bibtex">@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}, @@ -64,22 +125,22 @@ organization={Omnipress} } </citation> - <citation type="bibtex">@Article{Will_Joshi_Hofacker-LocAR_Accur_bound-2012, - author = {Will, Sebastian and Joshi, Tejal and Hofacker, Ivo L. and + <citation type="bibtex">@Article{Will_Joshi_Hofacker-LocAR_Accur_bound-2012, + author = {Will, Sebastian and Joshi, Tejal and Hofacker, Ivo L. and Stadler, Peter F. and Backofen, Rolf}, - title = {{LocARNA}-{P}: {Accurate} boundary prediction and improved + title = {{LocARNA}-{P}: {Accurate} boundary prediction and improved detection of structural {RNAs}}, - journal = {RNA}, - year = {2012}, - volume = {18}, - number = {5}, - pages = {900-14}, - user = {will}, - pmid = {22450757}, - doi = {10.1261/rna.029041.111}, - issn = {1469-9001}, - issn = {1355-8382}, - abstract = {Current genomic screens for noncoding RNAs (ncRNAs) predict + journal = {RNA}, + year = {2012}, + volume = {18}, + number = {5}, + pages = {900-14}, + user = {will}, + pmid = {22450757}, + doi = {10.1261/rna.029041.111}, + issn = {1469-9001}, + issn = {1355-8382}, + abstract = {Current genomic screens for noncoding RNAs (ncRNAs) predict a large number of genomic regions containing potential structural ncRNAs. The analysis of these data requires highly accurate prediction of ncRNA boundaries and @@ -110,14 +171,14 @@ for refining screens for structural ncRNA, at http://www.bioinf.uni-freiburg.de/Supplements/LocARNA-P/.} } - </citation> - <citation type="bibtex">@Article{Will:etal:_infer_non_codin_rna_famil:PLOS2007, - author = {Sebastian Will and Kristin Reiche and Ivo L. Hofacker and + </citation> + <citation type="bibtex">@Article{Will:etal:_infer_non_codin_rna_famil:PLOS2007, + author = {Sebastian Will and Kristin Reiche and Ivo L. Hofacker and Peter F. Stadler and Rolf Backofen}, - title = {Inferring Non-Coding {RNA} Families and Classes by Means of + title = {Inferring Non-Coding {RNA} Families and Classes by Means of Genome-Scale Structure-Based Clustering}, - journal = {PLoS Comput Biol}, - year = 2007, + journal = {PLoS Comput Biol}, + year = 2007, volume = {3}, number = {4}, pages = {e65}, @@ -125,8 +186,8 @@ issn = {1553-734X}, pmid = {17432929}, doi = {10.1371/journal.pcbi.0030065}, - user = {will}, - abstract = {The RFAM database defines families of ncRNAs by means of + user = {will}, + abstract = {The RFAM database defines families of ncRNAs by means of sequence similarities that are sufficientto establish homology. In some cases, such as microRNAs, box H/ACA snoRNAs, functional commonalities define classes of RNAs @@ -160,23 +221,23 @@ characterized.} } - </citation> - <citation type="bibtex">@Article{Smith:Heyne:Richter:Freib_RNA_Tools:NAR2010, - author = {Smith, Cameron and Heyne, Steffen and Richter, Andreas S. + </citation> + <citation type="bibtex">@Article{Smith:Heyne:Richter:Freib_RNA_Tools:NAR2010, + author = {Smith, Cameron and Heyne, Steffen and Richter, Andreas S. and Will, Sebastian and Backofen, Rolf}, - title = {Freiburg {RNA} {Tools}: a web server integrating {IntaRNA}, + title = {Freiburg {RNA} {Tools}: a web server integrating {IntaRNA}, {ExpaRNA} and {LocARNA}}, - journal = NAR, - year = {2010}, - volume = {38 Suppl}, - number = {}, - pages = {W373-7}, - user = {arichter}, - pmid = {20444875}, - doi = {10.1093/nar/gkq316}, - issn = {0305-1048}, - issn = {1362-4962}, - abstract = {The Freiburg RNA tools web server integrates three tools + journal = NAR, + year = {2010}, + volume = {38 Suppl}, + number = {}, + pages = {W373-7}, + user = {arichter}, + pmid = {20444875}, + doi = {10.1093/nar/gkq316}, + issn = {0305-1048}, + issn = {1362-4962}, + abstract = {The Freiburg RNA tools web server integrates three tools for the advanced analysis of RNA in a common web-based user interface. The tools IntaRNA, ExpaRNA and LocARNA support the prediction of RNA-RNA interaction, exact RNA matching @@ -185,6 +246,6 @@ tools are freely accessible at http://rna.informatik.uni-freiburg.de.} } - </citation> - </citations> + </citation> + </citations> </tool>