diff rnasubopt.xml @ 0:78d673470d45 draft

Imported from capsule None

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rnasubopt.xml	Wed Feb 04 12:05:27 2015 -0500
@@ -0,0 +1,126 @@
+<tool id="rnasubopt" name="RNAsubopt" version="2.1.6.0">
+    <description>Calculates suboptimal secondary structures of RNAs</description>
+    <expand macro="requirements" />
+    <expand macro="version_command" />
+    <expand macro="stdio" />
+    <macros>
+        <token name="@EXECUTABLE@">RNAsubopt</token>
+        <import>macros.xml</import>
+    </macros>
+    <command>
+<![CDATA[
+        RNAsubopt < $input > $output
+        -T$temperature
+        --dangles=$dangling
+        #if $methodOption.methodSelector == "range"
+            --deltaEnergy=$methodOption.deltaenergy
+        #else
+            --stochBT=$methodOption.stochastic
+        #end if
+        #if $outputOption.outputSelector == "yes"
+            --deltaEnergyPost=$deltaenergypost
+        #end if
+        $constraint
+        $sorted
+        $dos
+        $zuker
+        #if $varExists('$advancedOptions.nolp')
+            $advancedOptions.noconv
+            $advancedOptions.nolp
+            $advancedOptions.nogu
+            $advancedOptions.noclosinggu
+            $advancedOptions.notetra
+            $advancedOptions.logml
+        #end if
+]]>
+    </command>
+
+    <inputs>
+        <param format="fasta" name="input" type="data" label="Fasta file"/>
+        <param name="temperature" size="8" 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="2" selected="true">unpaired bases participate in all dangling ends (2)</option>
+            <option value="0">ignore dangling ends (0)</option>
+            <option value="1">unpaired bases participate in one dangling end only (1)</option>
+            <option value="3">allow coaxial stacking (3)</option>
+        </param>
+        <param name="constraint" type="boolean" truevalue="--constraint" falsevalue="" checked="false" label="Constraints for the secondary structure" help="--constraint"/>
+        <param name="sorted" type="boolean" truevalue="--sorted" falsevalue="" checked="false" label="Sort the secondary structures by energy" help="--sorted"/>
+        <param name="dos" type="boolean" truevalue="--dos" falsevalue="" checked="false" label="Calculate the density of states instead of the structure" help="--dos"/>
+        <param name="zuker" type="boolean" truevalue="--zuker" falsevalue="" checked="false" label="Calculate the Zuker suboptimals instead of the structures within a range." help="--zuker"/>
+
+        <conditional name="methodOption">
+            <param name="methodSelector" type="select" label="select algorithm">
+                <option value="range" selected="true">energy range</option>
+                <option value="stochastic">choose stochastically</option>
+            </param>
+            <when value="stochastic">
+                <param name="stochastic"  type="integer" value="1" label="Calculate this number of suboptimal structures chosen stochastically" help="--stochBT"/>
+            </when>
+            <when value="range">
+                <param name="deltaenergy" size="8" type="float" value="1.0" label="Range of energy for the suboptimal structures." help="--deltaEnergy"/>
+            </when>
+        </conditional>
+
+        <conditional name="outputOption">
+            <param name="outputSelector" type="select" label="select output restriction">
+                <option value="no" selected="true">no restriction</option>
+                <option value="yes">restricted output</option>
+            </param>
+            <when value="no"/>
+            <when value="yes">
+                <param name="deltaenergypost" size="8" type="float" value="0.0" label="Print only those structures that have a smaller difference in energy than the mfe." help="--deltaEnergyPost"/>
+            </when>
+        </conditional>
+
+        <conditional name="advancedOptions">
+            <param name="advancedSelector" type="select" label="advanced options">
+                <option value="basic">basic Options</option>
+                <option value="advanced">advanced Options</option>
+            </param>
+            <when value="advanced">
+                <param name="circ" type="boolean" truevalue="--circ" falsevalue="" checked="false" label="Assume circular RNA structure" help="--circ"/>
+                <param name="noconv" type="boolean" truevalue="--noconv" falsevalue="" checked="false" label="No conversion of T -> U" help="--noconv"/>
+                <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="logml" type="boolean" truevalue="--logML" falsevalue="" checked="false" label="Recalculate energies of structures using a logarithmic energy function for multi-loops" help="--logML"/>
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data format="txt" name="output"/>
+    </outputs>
+    <tests>
+    </tests>
+    <help>
+<![CDATA[
+
+**RNAsubopt**
+
+In the default -e mode RNAsubopt calculates all suboptimal secondary structures within a user defined energy range above the minimum free energy (mfe). It prints the suboptimal structures in dot-bracket notation followed by the energy in kcal/mol to stdout. Be careful, the number of structures returned grows exponentially with both sequence length and energy range.
+
+Alternatively, when used with the -p option, RNAsubopt produces Boltzmann weighted samples of secondary structures.
+
+
+-----
+
+**Input format**
+
+RNAsubopt requires one input file
+
+- fasta file
+
+
+------
+
+**Outputs**
+
+- secondary structure in dot-bracket format
+
+
+]]>
+    </help>
+    <expand macro="requirements" />
+</tool>