# HG changeset patch
# User yhoogstrate
# Date 1434468072 14400
# Node ID bf022d3751fa8ecd02942a85d94159f10165379a

planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/unafold_galaxy_wrapper commit 84b70c01144fa018db45215941fb395798376100-dirty

diff -r 000000000000 -r bf022d3751fa datatypes_conf.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/datatypes_conf.xml	Tue Jun 16 11:21:12 2015 -0400
@@ -0,0 +1,25 @@
+<?xml version="1.0"?>
+<datatypes>
+    <datatype_files>
+        <datatype_file name="RNAStructure.py"/>
+    </datatype_files>
+
+    <registration>
+        <datatype
+            extension="ct"
+            type="galaxy.datatypes.RNAStructure:ConnectivityTable"
+            display_in_upload="True"
+            subclass="True"
+            description="ConnectivityTable format is a text-based column wise format for storing both an RNA sequence and its corresponding 2D structure." />
+        <datatype
+            extension="rnaml"
+            type="galaxy.datatypes.RNAStructure:RNAML"
+            display_in_upload="True"
+            subclass="True"
+            description="RNAML: a standard syntax for exchanging RNA information."
+            url="http://www.ncbi.nlm.nih.gov/pubmed/12088144" />
+    </registration>
+    
+    <sniffers>
+    </sniffers>
+</datatypes>
diff -r 000000000000 -r bf022d3751fa lib/galaxy/datatypes/RNAStructure.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/lib/galaxy/datatypes/RNAStructure.py	Tue Jun 16 11:21:12 2015 -0400
@@ -0,0 +1,132 @@
+import logging
+log = logging.getLogger(__name__)
+
+from galaxy import util
+import galaxy
+import galaxy.model
+import galaxy.datatypes
+import galaxy.datatypes.data
+
+from galaxy.datatypes.metadata import MetadataElement
+
+from galaxy.datatypes.sequence import Sequence
+from galaxy.datatypes.tabular import Tabular
+from galaxy.datatypes.xml import GenericXml
+
+from galaxy.datatypes.data import Data
+
+
+import re
+
+class DotBracket ( Sequence ):
+    edam_format = "format_1457"
+    file_ext = "dbn"
+    
+    sequence_regexp = re.compile( "^[ACGTURYKMSWBDHVN]*" )
+    structure_regexp = re.compile( "^[\(\)\.]*" )
+    
+    def set_meta( self, dataset, **kwd ):
+        """
+        Set the number of sequences and the number of data lines
+        in dataset.
+        """
+        if self.max_optional_metadata_filesize >= 0 and dataset.get_size() > self.max_optional_metadata_filesize:
+            dataset.metadata.data_lines = None
+            dataset.metadata.sequences = None
+            dataset.metadata.seconday_structures = None
+            return
+        
+        data_lines = 0
+        sequences = 0
+        
+        for line in file( dataset.file_name ):
+            line = line.strip()
+            data_lines += 1
+            
+            if line and line.startswith( '>' ):
+                sequences += 1
+        
+        dataset.metadata.data_lines = data_lines
+        dataset.metadata.sequences = sequences
+    
+    def sniff(self, filename):
+        """
+        The format is as follows, although it remains unclear whether
+        the Dot-Bracket format may contain multiple sequences per file:
+        
+        >sequenceName1
+        CCCaaaGGG
+        (((...)))
+        >sequenceName2
+        GGGuuuCCC
+        (((...)))
+        """
+        
+        i = 0
+        pairs = False
+        
+        with open( filename ) as handle:
+            for line in handle:
+                line = line.strip()
+                
+                state = i % 3
+                
+                if state == 0:#header line
+                    if(line[0] != '>'):
+                        return False
+                elif state == 1:#sequence line
+                    if not sequence_regexp.match(line.upper()):
+                        return False
+                    else:
+                        sequence_size = len(line)
+                elif state == 2:#dot-bracket structure line
+                    if (sequence_size != len(line)) or (not structure_regexp.match(line)):
+                        return False
+                
+                i += 1
+        return True
+
+class ConnectivityTable( Tabular ):
+    edam_format = "format_3309"
+    file_ext = "ct"
+    
+    header_regexp = re.compile( "^[0-9]+" + "(?:\t|[ ]+)" + "[^ \t]+")
+    structure_regexp = re.compile( "^[0-9]+" + "(?:\t|[ ]+)" +  "[ACGTURYKMSWBDHVN]+" + "(?:\t|[ ]+)" + "[^\t]+" + "(?:\t|[ ]+)" + "[^\t]+" + "(?:\t|[ ]+)" + "[^\t]+" + "(?:\t|[ ]+)" + "[^\t]+")
+    
+    def __init__(self, **kwd):
+        Tabular.__init__( self, **kwd )
+        
+        self.columns = 6
+        self.column_names = ['base_index', 'base', 'neighbor_left', 'neighbor_right', 'partner', 'natural_numbering']
+        self.column_types = ['int', 'str', 'int', 'int', 'int', 'int']
+
+    def set_meta( self, dataset, **kwd ):
+        data_lines = 0
+        
+        for line in file( dataset.file_name ):
+            data_lines += 1
+        
+        dataset.metadata.data_lines = data_lines
+    
+    def sniff(self, filename):
+        
+        filename = filename.file_name
+        
+        i = 0
+        with open( filename ) as handle:
+            for line in handle:
+                line = line.strip()
+                
+                if(i == 0):
+                    if not self.header_regexp.match(line):
+                        return False
+                else:
+                    if not self.structure_regexp.match(line.upper()):
+                        return False
+                i += 1
+        return True
+
+
+class RNAML( GenericXml ):
+    edam_format = "format_3311"
+    file_ext = "rnaml"
diff -r 000000000000 -r bf022d3751fa test-data/test1_input.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test1_input.fa	Tue Jun 16 11:21:12 2015 -0400
@@ -0,0 +1,2 @@
+>seq1
+GGGGGaaaCCCCC
\ No newline at end of file
diff -r 000000000000 -r bf022d3751fa test-data/test1_output.ct
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test1_output.ct	Tue Jun 16 11:21:12 2015 -0400
@@ -0,0 +1,14 @@
+13	dG = -8.9	seq1
+1	G	0	2	12	1	0	2
+2	G	1	3	11	2	1	3
+3	G	2	4	10	3	2	4
+4	G	3	5	9	4	3	0
+5	G	4	6	0	5	0	0
+6	a	5	7	0	6	0	0
+7	a	6	8	0	7	0	0
+8	a	7	9	0	8	0	0
+9	C	8	10	4	9	0	10
+10	C	9	11	3	10	9	11
+11	C	10	12	2	11	10	12
+12	C	11	13	1	12	11	13
+13	C	12	0	0	13	12	0
diff -r 000000000000 -r bf022d3751fa tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Tue Jun 16 11:21:12 2015 -0400
@@ -0,0 +1,6 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="unafold" version="3.8">
+        <repository changeset_revision="9d157819abe5" name="package_unafold_3_8" owner="yhoogstrate" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+</tool_dependency>
diff -r 000000000000 -r bf022d3751fa unafold.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/unafold.xml	Tue Jun 16 11:21:12 2015 -0400
@@ -0,0 +1,101 @@
+<?xml version="1.0"?>
+<tool id="unafold" name="UNAFold" version="1.0.0">
+    <description>UNAFold RNA and DNA structure prediction</description>
+    
+    <requirements>
+        <requirement type="package" version="3.8">unafold</requirement>
+    </requirements>
+    
+    <stdio>
+        <regex match="mv: cannot stat ..: No such file or directory" source="stderr" level="fatal" description="Could not find CT output file\n" />
+    </stdio>
+    
+    <version_command>UNAFold.pl --version</version_command>
+    
+    <command>
+        UNAFold.pl
+            -n $n.a
+            -t $temp
+            
+            #if $n.a == "DNA"
+                -N $sodium
+                -M $magnesium
+            #end if
+        
+        $input_file &amp;&amp;
+        output=\$(ls | grep &#92;.ct | sort -r | head -n 1) &amp;&amp;
+        mv "\$output" "$output_ct"
+    </command>
+    
+    <inputs>
+        <param format="fasta" name="input_file" type="data" label="Input sequence (FASTA)"/>
+    
+        <conditional name="n">
+            <param name="a" type="select" label="Nucleic Acid Type">
+                <option value="RNA" selected="true">RNA</option>
+                <option value="DNA">DNA</option>
+            </param>
+            
+            <when value="RNA">
+            </when>
+            <when value="DNA">
+                <param name="sodium" type="float" size="6" value="1.0" min="0" max="100" label="[Na+] in M"/>
+                <param name="magnesium" type="float" size="6" value="0.0" min="0" max="100" label="[Mg++] in M"/>
+            </when>
+        </conditional>
+        
+        <param name="temp" type="integer" size="3" value="37" min="0" max="100" label="Temperature (&#176;C)"/>
+    </inputs>
+    
+    <outputs>
+        <data format="ct" name="output_ct" label="${tool.name} on ${input_file.hid}: ${input_file.name}"/>
+    </outputs>
+    
+    <tests>
+        <test>
+            <param name="input_file" value="test1_input.fa" ftype="fasta" />
+            <param name="temp" value="37" />
+            
+            <output name="output_ct" file="test1_output.ct" />
+        </test>
+    </tests>
+
+    <help>
+        Usage: UNAFold.pl [options] file [file]
+
+        Options:
+        -V, --version
+        -h, --help
+        -n, --NA=(RNA | DNA) (defaults to RNA)
+        -t, --temp=&lt;temperature&gt; (defaults to 37)
+        -N, --sodium=&lt;[Na+] in M&gt; (defaults to 1)
+        -M, --magnesium=&lt;[Mg++] in M&gt; (defaults to 0)
+        -p, --polymer
+        -C, --Ct=&lt;total strand concentration&gt;
+        -I, --noisolate
+        -m, --maxbp=&lt;maximum basepair distance&gt;
+        -c, --constraints=&lt;name of constraints file&gt; (defaults to prefix.aux)
+        -P, --percent=&lt;energy increment percent&gt; (defaults to 5)
+        -W, --window=&lt;window size&gt; (default set by sequence length)
+        -X, --max=&lt;maximum number of foldings&gt; (defaults to 100)
+            --ann=(none | p-num | ss-count) (defaults to none)
+            --mode=(auto | bases | lines) (defaults to auto)
+            --label=&lt;base numbering frequency&gt;
+            --rotate=&lt;structure rotation angle&gt;
+            --run-type=(text | html) (defaults to text)
+            --model=(EM | PF) (defaults to EM)
+            --circular
+        Obscure options:
+            --allpairs
+            --maxloop=&lt;maximum bulge/interior loop size&gt; (defaults to 30)
+            --nodangle
+            --simple
+            --prefilter=&lt;filter value&gt;
+
+        Report bugs to markhn@rpi.edu
+    </help>
+    
+    <citations>
+        <citation type="doi">10.1007/978-1-60327-429-6_1</citation>
+    </citations>
+</tool>