Mercurial > repos > rnateam > kinwalker
changeset 1:643da63cb382 draft default tip
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/kinwalker commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
| author | rnateam |
|---|---|
| date | Wed, 12 Jul 2017 14:10:44 -0400 |
| parents | cb66f1d643e4 |
| children | |
| files | README.md kinwalker.xml test-data/mfe_struct_result.fasta test-data/test_sequence_input.fasta test-data/trajectory_result.tabular tool_dependencies.xml |
| diffstat | 6 files changed, 1 insertions(+), 198 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.md Wed Jul 12 14:10:44 2017 -0400 @@ -0,0 +1,1 @@ +This tool is now included in the viennarna suite
--- a/kinwalker.xml Thu Feb 26 12:40:03 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,145 +0,0 @@ -<tool id="rbc_kinwalker" name="Kinwalker" version="1.0"> - <description> -<![CDATA[ -cotranscriptional folding of RNAs -]]> - </description> - <requirements> - <requirement type="package" version="1.0">kinwalker</requirement> - <requirement type="package" version="8.22">gnu_coreutils</requirement> - <requirement type="package" version="2.1">vienna_rna</requirement> - </requirements> - <command> -<![CDATA[ - head -n 1 $input_sequence | head -c -1 -q > seq.ident - && - sed '1d' $input_sequence > input.seq - && - kinwalker - $init_structure - $interrupt - ##$printfront - - --barrier_heuristic $barrier_heuristic.used - - #if $barrier_heuristic.used == "M" - --grouping $barrier_heuristic.grouping - --lookahead $barrier_heuristic.lookahead - #else if $barrier_heuristic.used == "B" - --maxkeep $barrier_heuristic.maxkeep - #end if - - --dangle $dangle - --noLonelyPairs $noLonelyPairs - --transcribed $transcribed - --transcription_rate $transcription_rate - --windowsize $windowsize - - < input.seq - - > blah - - && - sed -n '2s/[\.\(\)]\+\s\+\(.\+\)$/ mfe: \1/p' blah > energy - - && - cat seq.ident energy > $mfe_struct - - && - sed -e '2s/^\([\.\(\)]\+\).*$/\1/' -ne '1,2p' blah >> $mfe_struct - - && - sed -e 's/[ \t]*$//' -ne '/TRAJ/,/Kinwal/ {/TRAJ/n;/Kinwal/!{s/\s/\t/gp}}' blah > $trajectory -]]> - </command> - <stdio> - <!-- Anything other than zero is an error --> - <exit_code range="1:" /> - <exit_code range=":-1" /> - <!-- In case the return code has not been set propery check stderr too --> - <regex match="Error:" /> - <regex match="Exception:" /> - </stdio> - <inputs> - <param name="input_sequence" format="fasta" type="data" label="Input sequence" help="A single sequence in FASTA format"/> - <param name="init_structure" type="boolean" truevalue="--init_structure" falsevalue="" checked="false" label="Start with a structure other than the open chain" help="(--init_structure)"/> - <param name="interrupt" type="boolean" truevalue="--interrupt" falsevalue="" checked="false" label="Allow interrupted folding trajectories when the barrier is exceeded" help="(--interrupt)"/> - <!-- need to implement with dataset collections <param name="printfront" type="boolean" truevalue="!doublehypen!printfront" falsevalue="" checked="true" label="Creates PS plots of front progression" help="(!doublehypen!printfront)"/> --> - <conditional name="barrier_heuristic"> - <param name="used" type="select" label="Barrier Heuristic" help="(--barrier_heuristic)"> - <option value="M" selected="true">Morgan-Higgs</option> - <option value="S">Limit small stacks</option> - <option value="B">Barriers</option> - <option value="A">All</option> - </param> - <when value="M"> - <param name="grouping" type="select" label="How to treat conflict groups" help="(--grouping)"> - <option value="standard" selected="true">Standard</option> - <option value="regroup">Re-group</option> - </param> - <param name="lookahead" type="integer" value="1" label="Number of basepairs that MorganHiggs forms its subpaths from" help="(--lookahead)"/> - </when> - <when value="S" /> - <when value="B"> - <param name="maxkeep" type="integer" value="1" label="Breadth of breadth first search" help="(--maxkeep)"/> - </when> - <when value="A" /> - </conditional> - <param name="dangle" type="select" label="Dangle value as in VienneRNA package" help="(--dangle)"> - <option value="0" selected="true">0</option> - <option value="1">1</option> - <option value="2">2</option> - </param> - <param name="noLonelyPairs" type="integer" value="2" label="Value of noLonelyPairs as in ViennaRNA" help="(--noLonelyPairs)"/> - - <param name="transcribed" type="integer" value="1" label="Number of bases initially transcribed" help="0 means all is transcribed (--transcribed)"/> - <param name="transcription_rate" type="float" value="200" label="Number of bases transcribed per second" help="(--transcription_rate)"/> - <param name="windowsize" type="integer" value="0" label="Max size of substructures considered for folding events during transcription" help="0= all are considered. (--windowsize)"/> - </inputs> - <outputs> - <data format="fasta" name="mfe_struct" label="MFE structure from ${tool.name} on ${on_string}" /> - <data format="tabular" name="trajectory" label="Trajectory of ${tool.name} on ${on_string}" /> - </outputs> - <tests> - <test> - <param name="input_sequence" value="test_sequence_input.fasta" /> - <param name="init_structure" value="" /> - <param name="interrupt" value="" /> - <param name="used" value="M" /> - <param name="grouping" value="standard" /> - <param name="lookahead" value="1" /> - <param name="dangle" value="0" /> - <param name="noLonelyPairs" value="2" /> - <param name="transcribed" value="1" /> - <param name="transcription_rate" value="200" /> - <param name="windowsize" value="0" /> - <output name="mfe_struct" file="mfe_struct_result.fasta" /> - <output name="trajectory" file="trajectory_result.tabular" /> - </test> - </tests> - <help> -<![CDATA[ -**What Kinwalker does** - -Kinwalker splits the folding process into a series of events where each event can either be a folding event or a transcription event. -In each transcription event one base from the RNA sequence is appended to the already transcribed and (partially) folded subsequence. -Kinwalker executes transcription events at regular time intervals. In each folding event a subsequence of the already transcribed -RNA sequence is selected and a new structure is formed by combining base pairs from the current structure with base pairs from the -mfE structure of that subsequence. - -This is done in such a way that the new structure includes base pairs from both structures in an energetically favorable manner. -Kinwalker estimates the waiting times for individual folding events depending on the height of the energy barrier between the -current structure and the new structure into which the molecule is folded. Folding events between structures can only occur, -if the energy barrier between them is less than the maximum allowed energy barrier. - -As folding paths can only be calculated exhaustively for short sequences (n>100), heuristic approaches have to be employed which explicitly -construct a (re)folding path between the two structures. The saddle height is then estimated as the highest point along the path. -The best known algorithm for approximating saddle heights between RNA conformations is the Morgan-Higgs heuristic, -which tries to find a folding path from an origin secondary structure to a target secondary structure where the maximum height -along the path is minimal. The heuristic models state transitions at base pair resolution. -]]> - </help> - <citations> - <citation type="doi">10.1016/j.jmb.2008.02.064</citation> - </citations> -</tool>
--- a/test-data/mfe_struct_result.fasta Thu Feb 26 12:40:03 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,3 +0,0 @@ ->test_seq mfe: -13.6 -ACAGGUUCGCCUGUGUUGCGAACCUGCGGGUUCG -.(((((((((.......)))))))))........
--- a/test-data/test_sequence_input.fasta Thu Feb 26 12:40:03 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,2 +0,0 @@ ->test_seq -ACAGGUUCGCCUGUGUUGCGAACCUGCGGGUUCG
--- a/test-data/trajectory_result.tabular Thu Feb 26 12:40:03 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,10 +0,0 @@ -..(((....))) -0.4 0.0550686 3.9 6.46108 12 -.((((....)))) -3 0.0600001 5.96046e-09 6.46108 13 -(((((....))))) -4.7 0.065 0 6.46108 14 -(((((....)))))..((((....)))) -5.3 0.135069 3.9 6.46108 28 -(((((....))))).(((((....))))) -5.8 0.14 1.90735e-07 6.46108 29 -(((((....))))).......(((....)))... -6.9 0.17246 6.7 7.46108 34 -(((((....)))))......((((....)))).. -7.8 0.17246 9.53674e-08 7.46108 34 -(((((....))))).....(((((....))))). -10.7 0.17246 1.90735e-07 7.46108 34 -(((((....)))))....((((((....)))))) -13.1 0.17246 -1.90735e-07 7.46108 34 -.(((((((((.......)))))))))........ -13.6 123.457 12.5 13 34
--- a/tool_dependencies.xml Thu Feb 26 12:40:03 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,38 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="vienna_rna" version="2.1"> - <repository changeset_revision="3b53eda26527" name="package_vienna_rna_2_1" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="gnu_coreutils" version="8.22"> - <repository changeset_revision="ac64dfe4b1fb" name="package_gnu_coreutils_8_22" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="kinwalker" version="1.0"> - <install version="1.0"> - <actions> - <action target_filename="kinwalker.tar.gz" type="download_by_url">https://raw.githubusercontent.com/bgruening/download_store/master/kinwalker/kinwalker-patched.tar.gz</action> - <action type="set_environment_for_install"> - <repository changeset_revision="3b53eda26527" name="package_vienna_rna_2_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> - <package name="vienna_rna" version="2.1" /> - </repository> - </action> - <action type="shell_command">make VRNA_INC="-I$ROOT_VIENNA_RNA_DIR/include/ViennaRNA" VRNA_LIB="-L$ROOT_VIENNA_RNA_DIR/lib -lRNA" LDFLAGS="-fopenmp"</action> - <action type="move_file"> - <source>kinwalker</source> - <destination>$INSTALL_DIR/bin</destination> - </action> - <action type="set_environment"> - <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> - </action> - </actions> - </install> - <readme> - -The Kinwalker algorithm performs cotranscriptional folding of RNAs, -starting at a user a specified structure (default: open chain) and -ending at the minimum free energy structure. Folding events are -performed between transcription of additional bases and are regulated -by barrier heights between the source and target structure. - - </readme> - </package> -</tool_dependency>