# HG changeset patch
# User bgruening
# Date 1442524207 14400
# Node ID 42d20ff5da1b455797a739627abdb37d46de5342

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 1973f3035c10db80883d80847ea254289f5cce2a-dirty

diff -r 000000000000 -r 42d20ff5da1b dotknot.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/dotknot.xml	Thu Sep 17 17:10:07 2015 -0400
@@ -0,0 +1,140 @@
+<tool id="dotknot" name="DotKnot" version="1.3.1">
+    <description>pseudoknot prediction in a given RNA sequence</description>
+    <requirements>
+        <requirement type="package" version="1.8.5">vienna_rna</requirement>
+        <requirement type="package" version="1.3.1">dotknot</requirement>
+    </requirements>
+    <stdio>
+        <exit_code range="1:" />
+        <exit_code range=":-1" />
+        <regex match="Error:" />
+        <regex match="Exception:" />
+    </stdio>
+    <version_command>dotknot version 1.3.1</version_command>
+    <command><![CDATA[
+        cp \$DOTKNOT_ROOT_PATH/* ./ -R &&
+        dotknot.py
+        $input
+        $k
+        $l
+        $g
+        > ./output.txt
+        #if $g:
+            &&
+            mv ./*.ct ./globalstructure.ct
+        #end if
+    ]]></command>
+    <inputs>
+        <param name="input" type="data" format="fasta" label="Upload your FASTA file with RNA sequences:"
+            help="The FASTA file must contain a comment line starting with > followed by the sequence.
+                It can also contain several consecutive sequences and DotKnot will be executed for each sequence in the file."/>
+
+        <param argument="-k" type="boolean" checked="false"
+            truevalue="-k" falsevalue=""
+            label="Include kissing hairpins?"
+            help="Kissing hairpins are complex and biologically relevant types of pseudoknots.
+                Inclusion of kissing hairpins will lead to increased run time,
+                yet produce more meaningful results."/>
+
+        <param argument="-l" type="boolean" checked="false"
+            truevalue="-l" falsevalue=""
+            label="Include near-optimal local pseudoknots?"
+            help="Shows top five near-optimal local pseudoknots in terms of two criteria: 
+                estimated free energy to length ratio and lowest estimated free energy.
+                This can help to identify promising pseudoknot foldings and may
+                compensate for the limitations of the energy parameters."/>
+                
+         <param argument="-g" type="boolean" checked="false"
+            truevalue="-g" falsevalue=""
+            label="Include global structure?"
+            help="Shows predicted global structure in addition to predicted pseudoknots."/>
+
+    </inputs>
+    <outputs>
+            <data name="output" format="txt" from_work_dir="./output.txt" 
+                label="${tool.name} on ${on_string} (output file)">
+            </data>
+            <data name="outfile_globalstructure" format="txt" from_work_dir="./globalstructure.ct" 
+                label="${tool.name} on ${on_string} (output global structure)">
+                <filter>g == True</filter>
+            </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="TMV.fasta" ftype="fasta"/>
+            <param name="k" value=""/>
+            <param name="l" value=""/>
+            <param name="g" value=""/>
+            <output name="output" file="test1_output.txt" ftype="txt"/>
+        </test>
+        <test>
+            <param name="input" value="HCoV229E_short_KISSINGHAIRPINS.fasta" ftype="fasta"/>
+            <param name="k" value="-k"/>
+            <param name="l" value="-l"/>
+            <param name="g" value="-g"/>
+            <output name="output" file="test2_output.txt" ftype="txt"/>
+            <output name="outfile_globalstructure" file="test2_output2.ct" ftype="txt"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+**WHAT IT DOES**
+
+DotKnot is a heuristic method for pseudoknot prediction in a given RNA sequence.
+
+DotKnot extracts stem regions from the secondary structure probability dot plot calculated by RNAfold. Recursive H-type pseudoknots and intramolecular kissing hairpins are constructed and their presence in the sequence is verified. The detected pseudoknots can then be further analysed using bioinformatics or laboratory techniques.
+
+-----
+
+**INPUT**
+
+The FASTA file must contain a comment line starting with > followed by the sequence. It can also
+contain several consecutive sequences and DotKnot will be executed for each sequence in the file.
+
+Please ensure that only bases A,C,G,U,T (a,c,g,u,t) are used.
+
+*Example*::
+
+    > Arc-Ful-SRP short
+        GGGGGGUUCGGCGUCCCCUGUAACCCGAAACCGCCGAUACGCGGG
+    > MMTV
+        AAAAAACUUGUAAAGGGGCAGUCCCCUAGCCCCGCUCAAAAGGGGGAUG
+        
+-----
+
+**OPTIONAL ARGUMENTS**
+
+*Kissing hairpins*::
+    Kissing hairpins are complex and biologically relevant types of pseudoknots.
+    Inclusion of kissing hairpins will lead to increased run time, yet produce more meaningful
+    results.
+    
+*local pseudoknots*:: 
+    Shows top five near-optimal local pseudoknots in terms of two criteria: estimated free energy
+    to length ratio and lowest estimated free energy. This can help to identify promising pseudoknot
+    foldings and may compensate for the limitations of the energy parameters.
+*global structure*:: 
+    Shows predicted global structure in addition to predicted pseudoknots
+
+-----
+
+**OUTPUT**
+
+Each pseudoknot is displayed in dot-bracket notation. Unpaired bases are indicated by dots. Base
+pairs are written as bracket pairs. The first stem of a pseudoknot is indicated by round brackets , i.e. ( and ). The second stem of a pseudoknot is indicated by square brackets, i.e. [ and ]. 
+
+We also give the start and end positions of the pseudoknot with respect to the input sequence. If the global structure option is chosen (-g:), a CT file will be created which contains the global
+structure. The file name will start with the identifier given in the FASTA file.
+
+-----
+
+**dotknot** is a Free and Open Source Software, see more details and background information on the dotknot dotknot_ Website.
+
+.. _dotknot: http://dotknot.csse.uwa.edu.au/
+
+    ]]></help>
+    <citations>
+        <citation type="doi">10.1093/nar/gkq021</citation>
+        <citation type="doi">10.1261/rna.2394511</citation>
+    </citations>
+</tool>
diff -r 000000000000 -r 42d20ff5da1b test-data/HCoV229E_short_KISSINGHAIRPINS.fasta
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/HCoV229E_short_KISSINGHAIRPINS.fasta	Thu Sep 17 17:10:07 2015 -0400
@@ -0,0 +1,2 @@
+> PKB171 human coronavirus 229E, coronavirus; ribosomal frameshifting; polymerase
+CGGGGCUCUAGUGCCGCUCGACUAGAGCCCUGUAUGGACCACGAGCAGUCCAUG
\ No newline at end of file
diff -r 000000000000 -r 42d20ff5da1b test-data/TMV.fasta
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/TMV.fasta	Thu Sep 17 17:10:07 2015 -0400
@@ -0,0 +1,2 @@
+>TMV
+UGCAACUUGAGGUAGUCAAGAUGCAUAAUAAAUAACGGAUUGUGUCCGUAAUCACACGUGGUGCGUACGAUAACGCAUAGUGUUUUUCCCUCCACUUAAAUCGAAGGGUUGUGUCUUGGAUCGCGCGGGUCAAAUGUAUAUGGUUCAUAUACAUCCGCAGGCACGUAAUAAAGCGAGGGGUUCGAAUCCCCCCGUUACCCCCGGUAGGGGCCCA
diff -r 000000000000 -r 42d20ff5da1b test-data/test1_output.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test1_output.txt	Thu Sep 17 17:10:07 2015 -0400
@@ -0,0 +1,30 @@
+
+>TMV
+UGCAACUUGAGGUAGUCAAGAUGCAUAAUAAAUAACGGAUUGUGUCCGUAAUCACACGUGGUGCGUACGAUAACGCAUAGUGUUUUUCCCUCCACUUAAAUCGAAGGGUUGUGUCUUGGAUCGCGCGGGUCAAAUGUAUAUGGUUCAUAUACAUCCGCAGGCACGUAAUAAAGCGAGGGGUUCGAAUCCCCCCGUUACCCCCGGUAGGGGCCCA
+Sequence length:  214
+Using TMV as file identifier
+
+DotKnot is running...
+Predicting pseudoknots...
+
+Detected pseudoknots:
+35 56 -10.97
+ACGGAUUGUGUCCGUAAUCACA
+(((((.[[[[)))))...]]]]
+
+57 78 -12.92
+CGUGGUGCGUACGAUAACGCAU
+(((.[[[[[[)))...]]]]]]
+
+79 108 -8.16
+AGUGUUUUUCCCUCCACUUAAAUCGAAGGG
+((((.....[[[[.))))........]]]]
+
+111 176 -26.94
+GUGUCUUGGAUCGCGCGGGUCAAAUGUAUAUGGUUCAUAUACAUCCGCAGGCACGUAAUAAAGCGA
+((((((....[[[[((((((.....(((((((...)))))))))))))))))))........]]]]
+
+192 210 -13.83
+CCGUUACCCCCGGUAGGGG
+(((...[[[[)))..]]]]
+
diff -r 000000000000 -r 42d20ff5da1b test-data/test2_output.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test2_output.txt	Thu Sep 17 17:10:07 2015 -0400
@@ -0,0 +1,56 @@
+Include kissing hairpins.
+Show best local pseudoknots.
+Show predicted global structure.
+
+> PKB171 human coronavirus 229E, coronavirus; ribosomal frameshifting; polymerase
+CGGGGCUCUAGUGCCGCUCGACUAGAGCCCUGUAUGGACCACGAGCAGUCCAUG
+Sequence length:  54
+Using PKB171 as file identifier
+
+DotKnot is running...
+Predicting pseudoknots...
+Predicting kissing hairpins...
+
+Detected pseudoknots and kissing hairpins:
+1 54 -41.2
+CGGGGCUCUAGUGCCGCUCGACUAGAGCCCUGUAUGGACCACGAGCAGUCCAUG
+((((((((((((...[[[[[))))))))))))(((((((..]]]]].)))))))
+
+
+Best 5 pseudoknots and kissing hairpins in terms of energy to length ratio:
+1 54 -41.2
+CGGGGCUCUAGUGCCGCUCGACUAGAGCCCUGUAUGGACCACGAGCAGUCCAUG
+((((((((((((...[[[[[))))))))))))(((((((..]]]]].)))))))
+1 46 -26.23
+CGGGGCUCUAGUGCCGCUCGACUAGAGCCCUGUAUGGACCACGAGC
+((((((((((((...[[[[[)))))))))))).........]]]]]
+11 54 -18.12
+GUGCCGCUCGACUAGAGCCCUGUAUGGACCACGAGCAGUCCAUG
+(((..((((.....))))....[[[[[[[))).....]]]]]]]
+16 37 -7.79
+GCUCGACUAGAGCCCUGUAUGG
+((((..[[[))))......]]]
+11 48 -13.12
+GUGCCGCUCGACUAGAGCCCUGUAUGGACCACGAGCAG
+(((..((((.....)))).[[[[......)))..]]]]
+
+Best 5 pseudoknots and kissing hairpins in terms of free energy:
+1 54 -41.2
+CGGGGCUCUAGUGCCGCUCGACUAGAGCCCUGUAUGGACCACGAGCAGUCCAUG
+((((((((((((...[[[[[))))))))))))(((((((..]]]]].)))))))
+1 46 -26.23
+CGGGGCUCUAGUGCCGCUCGACUAGAGCCCUGUAUGGACCACGAGC
+((((((((((((...[[[[[)))))))))))).........]]]]]
+11 54 -18.12
+GUGCCGCUCGACUAGAGCCCUGUAUGGACCACGAGCAGUCCAUG
+(((..((((.....))))....[[[[[[[))).....]]]]]]]
+3 54 -16.6
+GGGCUCUAGUGCCGCUCGACUAGAGCCCUGUAUGGACCACGAGCAGUCCAUG
+(((......[[[.((((.....))))))).(((((((.....]]])))))))
+2 54 -16.2
+GGGGCUCUAGUGCCGCUCGACUAGAGCCCUGUAUGGACCACGAGCAGUCCAUG
+(((...........[[[[[.......)))..(((((((..]]]]].)))))))
+
+Predicted global structure
+CGGGGCUCUAGUGCCGCUCGACUAGAGCCCUGUAUGGACCACGAGCAGUCCAUG
+((((((((((((...[[[[[))))))))))))(((((((..]]]]].)))))))
diff -r 000000000000 -r 42d20ff5da1b test-data/test2_output2.ct
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test2_output2.ct	Thu Sep 17 17:10:07 2015 -0400
@@ -0,0 +1,55 @@
+54
+1 C 0 2 32 1 
+2 G 1 3 31 2 
+3 G 2 4 30 3 
+4 G 3 5 29 4 
+5 G 4 6 28 5 
+6 C 5 7 27 6 
+7 U 6 8 26 7 
+8 C 7 9 25 8 
+9 U 8 10 24 9 
+10 A 9 11 23 10 
+11 G 10 12 22 11 
+12 U 11 13 21 12 
+13 G 12 14 0 13 
+14 C 13 15 0 14 
+15 C 14 16 0 15 
+16 G 15 17 46 16 
+17 C 16 18 45 17 
+18 U 17 19 44 18 
+19 C 18 20 43 19 
+20 G 19 21 42 20 
+21 A 20 22 12 21 
+22 C 21 23 11 22 
+23 U 22 24 10 23 
+24 A 23 25 9 24 
+25 G 24 26 8 25 
+26 A 25 27 7 26 
+27 G 26 28 6 27 
+28 C 27 29 5 28 
+29 C 28 30 4 29 
+30 C 29 31 3 30 
+31 U 30 32 2 31 
+32 G 31 33 1 32 
+33 U 32 34 54 33 
+34 A 33 35 53 34 
+35 U 34 36 52 35 
+36 G 35 37 51 36 
+37 G 36 38 50 37 
+38 A 37 39 49 38 
+39 C 38 40 48 39 
+40 C 39 41 0 40 
+41 A 40 42 0 41 
+42 C 41 43 20 42 
+43 G 42 44 19 43 
+44 A 43 45 18 44 
+45 G 44 46 17 45 
+46 C 45 47 16 46 
+47 A 46 48 0 47 
+48 G 47 49 39 48 
+49 U 48 50 38 49 
+50 C 49 51 37 50 
+51 C 50 52 36 51 
+52 A 51 53 35 52 
+53 U 52 54 34 53 
+54 G 53 55 33 54 
diff -r 000000000000 -r 42d20ff5da1b test-data/tmRNA_alignment.fasta
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tmRNA_alignment.fasta	Thu Sep 17 17:10:07 2015 -0400
@@ -0,0 +1,11 @@
+>Ecoli-tmRNA
+GGGGCUGAUUCUGGAUUCGACGGGAUUUGCGAAACCCAAGGUGCAUGCCGAGGGGCGGUUGGCCUCGUAAAAAGCCGCAAAAAAUAGUCGCAAACGACGAAAACUACGCUUUAGCAGCUUAAUAACCUGCUUAGAGCCCUCUCUCCCUAGCCUCCGCUCUUAGGACGGGGAUCAAGAGAGGUCAAACCCAAAAGAGAUCGCGUGGAAGCCCUGCCUGGGGUUGAAGCGUUAAAACUUAAUCAGGCUAGUUUGUUAGUGGCGUGUCCGUCCGCAGCUGGCAAGCGAAUGUAAAGACUGACUAAGCAUGUAGUACCGAGGAUGUAGGAAUUUCGGACGCGGGUUCAACUCCCGCCAGCUCCACCA
+>Mesoplasma florum tmRNA
+GGGGAUGUCCUGGUUUCGACAGGAUACUCUGGUCAUAUAAUAGCAGUGGUGUGGUAGACCAUAAUACUUCUAGGUUUGAUAAAAUGCAAACAAAAACGAAGAAAACACAAACGAAGUUCCAACAUUUAUGUUAAAUGCUGGACAAGCAAAUUACGCUUUCGCUUAAUUUGACUUAAAUACAAAUAUACGUUUGGCAAUUUUUAAUAGUCUUGGAAUCUGUUAAUUAUUGUACAUACCAAUUCCAAUAGAAAUUAUGAUCGUAAUAAAUAAUUUUGAAACUCAAUUACGGAUGUUAUAUUAGUCUUUUGAUAAUUUUAUUUAAUAUAGCAAAUUAGAAAAUUAUCUAAACUGUAGAAUUUAUAUGAUUCGGUAUUUUGGACGUGGGUUCGAUUCCCACCAUCUCCACCA
+>Thermus thermophilus tmRNA, version 1 {HB8}: 
+GGGGGUGAAACGGUCUCGACGGGGGUCGCCGAGGGCGUGGCUGCGCGCCGAGGUGCGGGUGGCCUCGUAAAAACCCGCAACGGCAUAACUGCCAACACCAACUACGCUCUCGCGGCUUAAUGACCGCGACCUCGCCCGGUAGCCCUGCCGGGGGCUCACCGGAAGCGGGGACACAAACCCGGCUAGCCCGGGGCCACGCCCUCUAACCCCGGGCGAAGCUUGAAGGGGGCUCGCUCCUGGCCGCCCGUCCGCGGGCCAAGCCAGGAGGACACGCGAAACGCGGACUACGCGCGUAGAGGCCCGCCGUAGAGACCUUCGGACGGGGGUUCGACUCCCCCCACCUCCACCA
+>Actinobacillus actinomycetemcomitans tmRNA
+GGGGCUGAUUCUGGAUUCGACGGGAUUGGCGAAGCCCAAGGUGCACGUCGAGGUGCGGUAGGCCUCGUAAAUAAACCGCAAAAAAAUAGUCGCAAACGACGAACAAUACGCUUUAGCAGCUUAAUAACCUGCAUUUAGCCUUCGCUCCCCAGCUUCCGCUCGUAAGACGGGGAUCAAGCGGAGUCAAACCUAAACGAGAUCGUGUGGACGCUUCGGCUUGGAGAUCGAAACACUAAAUUGAAUCAAGCUAGUUUAUUCUUCGCGUGUCUGUCCGCAGGGGAUAAAUGAAGUUAAAGACCAGACUAAACGUGUAGUGCUGAAGGUAGAGUAAUUUCGGACGCGGGUUCAACUCCCGCCAGCUCCACCA
+>marine_actinobacteri.1 AAOB01000009.1/82671-83044
+GGGGAUGAUCGGUUUCGACAUUGCCUGCAAAACUGUGAGAAGCGGGUCGAGAAUGCAGCCUUAUCUCGUUAACGAUGACUGCAAACUAUAAGUGCCAAUUCAAAGCGCACUGACUUCGCCCUCGCUGCCUAAGCGAGCGCACUAAAGAAGUCCGUCAGACCGGGAAUGCUCUCUACCCGGAUCCUGGCGCAAUUUAGAGAGAUUGCUGCGUAGUUACGCCUGAGGGCUACGCGGGACUUGCACUCUGGCUGGGCUUGUUGAUCUAGGUGCUUGUGGCAAAGAUCAGAGCCGAGUAGAACGUCUGCACAAGCUACACCCGUAGAAGGCACAGAAUUACAGCAGUGGACGGGGGUUCAAUUCCCCCCAUCUCCACC
+
diff -r 000000000000 -r 42d20ff5da1b tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Thu Sep 17 17:10:07 2015 -0400
@@ -0,0 +1,27 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="vienna_rna" version="1.8.5">
+        <repository changeset_revision="6757330f89cd" name="package_vienna_rna_1_8" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="dotknot" version="1.3.1">
+        <install version="1.0">
+            <actions>
+                <action type="download_by_url">https://github.com/bgruening/download_store/raw/master/dotknot/dotknot_1.3.1.tar.bz2</action>
+                <action type="move_directory_files">
+                    <source_directory>.</source_directory>
+                    <destination_directory>$INSTALL_DIR</destination_directory>
+                </action>
+                <action type="set_environment">
+                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR</environment_variable>
+                    <environment_variable action="set_to" name="DOTKNOT_ROOT_PATH">$INSTALL_DIR</environment_variable>
+                </action>
+            </actions>
+        </install>
+            <readme>
+        
+            DotKnot:a heuristic method for pseudoknot prediction in a given RNA sequence.
+            See http://dotknot.csse.uwa.edu.au/
+        
+        </readme>
+    </package>
+</tool_dependency>