diff rnafold.xml @ 0:78d673470d45 draft

Imported from capsule None

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rnafold.xml	Wed Feb 04 12:05:27 2015 -0500
@@ -0,0 +1,125 @@
+<tool id="rnafold" name="RNAfold" version="2.1.6.0">
+    <description>Calculate minimum free energy secondary structures and partition function of RNAs</description>
+    <expand macro="requirements" />
+    <expand macro="version_command" />
+    <expand macro="stdio" />
+    <macros>
+        <token name="@EXECUTABLE@">RNAfold</token>
+        <import>macros.xml</import>
+    </macros>
+    <command>
+ <![CDATA[
+    RNAfold
+    -T $temperature
+    --dangles=$dangling
+    #if $measelect.mea == "yes":
+        --MEA=$measelect.meavalue
+    #else
+        $measelect.pf
+    #end if
+    #if $varExists('$advancedOptions.nogu'):
+        $advancedOptions.noconversion
+        $advancedOptions.gquad
+        $advancedOptions.nolp
+        $advancedOptions.nogu
+        $advancedOptions.noclosinggu
+        $advancedOptions.canonicalonly
+        $advancedOptions.circular
+    #end if
+
+    < $fasta_input
+
+    > $tabular_file
+]]>
+    </command>
+
+    <inputs>
+    <param format="fasta" name="fasta_input" type="data" label="FASTA file"/>
+        <param name="temperature" size="6" type="float" value="37.0" label="Temperature [°C]" help="-T"/>
+        <param name="dangling" type="select" label="how to treat dangling end energies" help="-d">
+            <option value="0">0: ignore dangling ends</option>
+            <option value="1">1: unpaired bases participate in one dangling end only</option>
+            <option value="2" selected="True">2: unpaired bases participate in all dangling ends</option>
+            <option value="3">3: allow coaxial stacking</option>
+        </param>
+        <conditional name="measelect">
+            <param name="mea" type="select" label="Calculate Maximum Expected accuracy" help="--MEA">
+                <option value="no">No</option>
+                <option value="yes">Yes</option>
+            </param>
+            <when value="yes">
+                <param name="meavalue" size="6" type="float" value="1.0" label="Gamma Value"/>
+            </when>
+            <when value="no">
+                <param name="pf" type="boolean" checked="false" truevalue="--partfunc" falsevalue="" label="Calculate Partition Function" help="--partfunc"/>
+            </when>
+        </conditional>
+        <conditional name="advancedOptions">
+            <param name="advancedSelector" type="boolean" checked="false" label=" advanced options"/>
+            <when value="true">
+                <param name="noconversion" type="boolean" truevalue="--noconv" falsevalue="" checked="false" label="no conversion" help="--noconv  do not convert thymine to uracile (T -> U)."/>
+                <param name="gquad" type="boolean" truevalue="--gquad" falsevalue="" checked="false" label="G Quadruplex formation" help="-g  take into account G Quadruplex formation"/>
+                <param name="nolp" type="boolean" truevalue="--noLP" falsevalue="" checked="false" label="No lonely pairs" help="--noLP  don't allow lonely pairs."/>
+                <param name="nogu" type="boolean" truevalue="--noGU" falsevalue="" checked="false" label="No GU pairing" help="--noGU  don't allow pairing of G and U."/> <param name="noclosinggu" type="boolean" truevalue="--noClosingGU" falsevalue="" checked="false" label="No GU pairing at the ends" help="--noClosingGU  don't allow pairing of G and U at the ends of helices."/> <param name="notetra" type="boolean" truevalue="--noTetra" falsevalue="" checked="false" label="No stabilization for loops, hairpins etc." help="--noTetra"/>
+                <param name="canonicalonly" type="boolean" truevalue="--canonicalBPonly" falsevalue="" checked="false" label="Canonical basepairing only" help="--canonicalBPonly"/>
+                <param name="circular" type="boolean" truevalue="--circ" falsevalue="" checked="false" label="Assume circular RNA structure" help="--circ"/>
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data format="tabular" name="tabular_file"/>
+        <collection name="sequence_outputs" type="list" label="rna_eps outputs">
+            <discover_datasets pattern="(?P&lt;designation&gt;.+)_ss\.ps" ext="eps" />
+        </collection>
+        <collection name="matrix_outputs" type="list" label="rna_eps outputs">
+            <filter>measelect['pf'] is True</filter>
+            <discover_datasets pattern="(?P&lt;designation&gt;.+)_dp\.ps" ext="rna_eps" visible="true"/>
+        </collection>
+          
+    </outputs>
+    <tests>
+    </tests>
+    <help>
+<![CDATA[
+**RNAfold**
+
+The program reads RNA sequences, calculates their minimum free
+energy (mfe) structure and the mfe structure in dot-bracket notation.
+
+If the -p option was given it also computes the
+partition function (pf) and base pairing probability matrix.
+
+The dot plot of the base pairing probability matrix shows a matrix of squares with area proportional to the pairing
+probability in the upper right half, and one square for each pair in the
+minimum free energy structure in the lower left half. For each pair i-j with
+probability p>10E-6 there is a line of the form
+
+i  j  sqrt(p)  ubox
+
+in the PostScript file, so that the pair probabilities can be easily extracted.
+
+The sequences have to be provided in FASTA format. The first word (max. 42 char) of the FASTA header will be used for output file names. PostScript files "name_ss.ps" and "name_dp.ps" are produced for the structure and dot plot, respectively.
+The program will read the whole FASTA input file and provide output for each found sequence.
+
+
+-----
+
+**Input format**
+
+RNAfold requires one input file
+- FASTA file
+
+------
+
+**Outputs**
+
+- Secondary structures in dot-bracket notation
+
+- several possible postscript images bundled together in a tar file
+    - secondary structure for each sequence in the input file
+    - if partition function is calculated (--MEA or --partfunc is set) then also the pairing probabilty matrix is generated for each sequence 
+
+]]>
+    </help>
+    <expand macro="citations" />
+</tool>