# HG changeset patch
# User rnateam
# Date 1499883084 14400
# Node ID 8f32d59f560684484077342a8e93447b93eed5d6
# Parent  723f1a32ad8599cd560d8aa3b425b4a180d61098
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/kinwalker commit 3103ebed1a420c7d3415b67ef532ea579edf9faa

diff -r 723f1a32ad85 -r 8f32d59f5606 README.md
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.md	Wed Jul 12 14:11:24 2017 -0400
@@ -0,0 +1,1 @@
+This tool is now included in the viennarna suite
diff -r 723f1a32ad85 -r 8f32d59f5606 kinwalker.xml
--- a/kinwalker.xml	Thu Feb 26 12:38:04 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>
diff -r 723f1a32ad85 -r 8f32d59f5606 test-data/mfe_struct_result.fasta
--- a/test-data/mfe_struct_result.fasta	Thu Feb 26 12:38:04 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,3 +0,0 @@
->test_seq mfe: -13.6
-ACAGGUUCGCCUGUGUUGCGAACCUGCGGGUUCG
-.(((((((((.......)))))))))........
diff -r 723f1a32ad85 -r 8f32d59f5606 test-data/test_sequence_input.fasta
--- a/test-data/test_sequence_input.fasta	Thu Feb 26 12:38:04 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,2 +0,0 @@
->test_seq
-ACAGGUUCGCCUGUGUUGCGAACCUGCGGGUUCG
diff -r 723f1a32ad85 -r 8f32d59f5606 test-data/trajectory_result.tabular
--- a/test-data/trajectory_result.tabular	Thu Feb 26 12:38:04 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
diff -r 723f1a32ad85 -r 8f32d59f5606 tool_dependencies.xml
--- a/tool_dependencies.xml	Thu Feb 26 12:38:04 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="bb91a5b178e2" name="package_vienna_rna_2_1" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="gnu_coreutils" version="8.22">
-        <repository changeset_revision="b638666e399d" name="package_gnu_coreutils_8_22" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.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="bb91a5b178e2" name="package_vienna_rna_2_1" owner="iuc" toolshed="https://testtoolshed.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>