--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/kinfold.xml	Tue Dec 06 12:35:17 2016 -0500
@@ -0,0 +1,104 @@
+<tool id="viennarna_kinfold" name="@EXECUTABLE@" version="1.3.0.0">
+    <description>Simulates the stochastic folding kinetics of RNA sequences into secondary structures.</description>
+    <macros>
+        <token name="@EXECUTABLE@">Kinfold</token>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="stdio" />
+    <expand macro="version_command" />
+    <command>
+<![CDATA[
+        Kinfold < '$input'
+        -T$Temp
+        --dangle=$dangle
+        $logML       
+        $move_set_options.noShift
+        $move_set_options.noLP
+        --num=$simulation_options.num
+        --time=$simulation_options.time
+        --grow=$simulation_options.grow
+        --glen=$simulation_options.glen
+        $simulation_options.fpt
+        $simulation_options.met
+        $output_options.lmin        
+        --cut=$output_options.cut
+        > '$output'
+        && cat *.log > '$log'
+]]>
+    </command>
+
+    <inputs>
+        <param format="*" name="input" type="data" label="Fasta file"/>
+        <param argument="--Temp" type="float" value="37.0" label="temperature [°C]"/>
+        <param argument="--dangle" type="select" label="how to treat dangling end energies">
+            <option value="0">0: none</option>
+            <option value="2" selected="true">2: double</option>
+            <option value="1">1: normal</option>
+        </param>
+        <param argument="--logML" type="boolean" truevalue="--logML" falsevalue="" checked="false" label="Logarithmic energy functions for multi-loops"/>
+        
+        <section name="move_set_options" title="Move set options">
+            <param argument="--noShift" type="boolean" truevalue="" falsevalue="--noShift" checked="true" label="Turn on shift moves."/>
+            <param argument="--noLP" type="boolean" truevalue="" falsevalue="--noLP" checked="true" label="Allow structures containing isolated base-pairs"/>
+        </section>
+        
+        <section name="simulation_options" title="Simulation options" >
+            <param argument="--num" type="integer" value="1" label="Number of trajectories to compute" help="" optional="true"/>
+            <param argument="--time" type="float" value="500.0" label="Set maximum length of folding trajectory" help="The default (500) is very short and meant for testing purposes only." optional="true"/>
+            <param argument="--grow" type="float" value="0" label="Simulate folding during transcription with a chain growth event taking place every rate timesteps." help="" optional="true"/>
+            <param argument="--glen" type="integer" value="15" label="Start a folding during transcription simulation with an inital chain length of len."  help="" optional="true" />
+            <param argument="--fpt" type="boolean" truevalue="--fpt" falsevalue="" checked="true" label="compute first passage time" help="stop when a stop-structure is reached"/>
+            <param argument="--met" type="boolean" truevalue="--met" falsevalue="" checked="false" label="Use the Metropolis rule for rate between two neighboring conformations" help="Use the Metropolis rule for rate between two neighboring conformations, i.e. k=min{1,exp(−dE/RT)}. By default Kinfold uses the symmetric Kawasaki rule k=exp(−dE/2RT)."/>
+        </section>
+        
+        <section name="output_options" title="Output Options">
+            <param argument="--lmin" type="boolean" truevalue="--lmin" falsevalue="" checked="false" label="Don’t print complete trajectory, but only local minimas encountered" help=""/>
+            <param argument="--cut" type="float" value="20.0" label="Cutoff energy" help="Print only those parts of the trajectory that stays below energy." optional="true"/>
+        </section>
+       
+    </inputs>
+    <outputs>
+        <data format="txt" name="output"/>
+        <data format="log" name="log"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="kinfold_input.txt"/>
+            <output name="output">
+                <assert_contents>
+                    <has_text text="..............." />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+
+**Kinfold**
+
+The program Kinfold simulates the stochastic folding kinetics of RNA sequences into secondary structures. Folding trajectories are simulated using a Monte Carlo procedure using the formation, and dissociation of individual base pairs, and (optionally) the shifting of individual base pairs.
+
+Note that all times are given in internal units that can be translated into real time only by copmparison with experiment. Very roughly one time step corresponds to about 1e−7 seconds.
+
+-----
+
+**Input format**
+
+Input consists of an RNA sequence, optionally followed by the initial structure and one or more stop structures in dot−bracket notation. 
+
+------
+
+**Outputs**
+
+- Trajecotires: 
+
+The trajectory lists stucture, energy, and time for each simulation step. The X1 signifies that the trajectory terminated in the first stop structure
+
+- A log file containing summary information for each trajectory:
+
+The logfile would contain information needed to reproduce the simulation results such as options and random seeds used.
+]]>
+    </help>
+    <expand macro="citations" />
+</tool>