Mercurial > repos > rnateam > graphclust_mlocarna
view locarna_best_subtree.xml @ 4:51261dff08a5 draft
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/LocARNAGraphClust commit f971832d2b34a182314e5201ea6895dd207c5923
author | rnateam |
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date | Mon, 13 Mar 2017 18:02:55 -0400 |
parents | 606440a3852d |
children | 859ee7d8f207 |
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<tool id="locarna_best_subtree" name="locarna_graphclust" version="0.1.0" > <requirements> <requirement type="package" version="0.1.10">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' '$tree_matrix' '$data_map' $allow_overlap $free_endgaps #if str($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="allow_overlap" type="boolean" truevalue="1" falsevalue="0" label="Allow overlap in subtrees" help="otherwise ignore subtree if it contains overlapping sequences"/> <param name="free_endgaps" type="select" label="Free endgaps" help="Specify whether gaps at the ends (all, 5', or 3' ends) of the sequences should be penalized or allowed for free."> <option value="0">No free endgaps</option> <option value="--free-endgaps">Free endgaps</option> <option value="--free-endgaps-5">Free endgaps, only 5'</option> <option value="--free-endgaps-3">Free endgaps, only 3'</option> </param> <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" /> <param name="plfold_winsize" type="integer" value="300" min="-1" max="800" label="Window size for local folding" /> </when> <when value="locarna" /> </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"/> <param name="allow_overlap" value="0"/> <param name="free_endgaps" value="0"/> <param name="param_type_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"/> <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. It uses *treefile* - file with guide tree in NEWICK format. The given tree is used as guide tree for the progressive alignment. This saves the calculation of pairwise all-vs-all similarities and construction of the guide tree. ]]> </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}, pages={255--262}, year={2010}, organization={Omnipress} } </citation> <citation type="doi">10.1261/rna.029041.111</citation> <citation type="doi">10.1371/journal.pcbi.0030065</citation> <citation type="doi">10.1093/nar/gkq316</citation> </citations> </tool>