diff rnaheat.xml @ 0:78d673470d45 draft

Imported from capsule None

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaheat.xml	Wed Feb 04 12:05:27 2015 -0500
@@ -0,0 +1,80 @@
+<tool id="rnaheat" name="RNAheat" version="2.1.6.0">
+    <description>Calculate energies of RNA in a temperature range</description>
+    <expand macro="requirements" />
+    <expand macro="version_command" />
+    <expand macro="stdio" />
+    <macros>
+        <token name="@EXECUTABLE@">RNAheat</token>
+        <import>macros.xml</import>
+    </macros>
+    <command>
+<![CDATA[
+        RNAheat < $input > $output
+        --Tmin $tmin --Tmax $tmax -d$dangling --stepsize=$stepsize --ipoints=$ipoints
+        #if $varExists('$advancedOptions.noconversion')
+            $advancedOptions.noconversion
+            $advancedOptions.nolp
+            $advancedOptions.nogu
+            $advancedOptions.noclosinggu
+            $advancedOptions.notetra
+        #end if
+]]>
+    </command>
+
+    <inputs>
+        <param format="fasta" name="input" type="data" label="Input file"/>
+        <param name="tmin" size="6" type="float" value="0.0" label="minimal temperature [°C]" help="--Tmin"/>
+        <param name="tmax" size="6" type="float" value="100.0" label="maximal temperature [°C]" help="--Tmax"/>
+        <param name="stepsize" size="6" type="float" value="1.0" label="stepsize [°C]" help="--stepsize"/>
+        <param name="ipoints" size="3" type="integer" value="2" label="data points to fit parabola to: 2*value+1" help="--ipoints"/>
+        <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="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="noconversion" type="boolean" truevalue="--noconv" falsevalue="" checked="false" label="no conversion" help="--noconv  do not convert thymine to uracile (T -> U)."/>
+                <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"/>
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data format="txt" name="output"/>
+    </outputs>
+    <tests>
+    </tests>
+    <help>
+<![CDATA[
+**RNAheat**
+
+Calculates the specific heat of RNA sequences in the temperature range t1 to t2, from the partition function by numeric differentiation. The program fits a parabola to 2*ipoints+1 data points to calculate 2nd derivatives. Increasing this parameter produces a smoother curve.
+
+
+-----
+
+**Input format**
+
+RNAheat requires one input file Fasta format.
+
+
+------
+
+**Outputs**
+
+The result is written as a list of pairs of temperature in C and specific heat in Kcal/(Mol*K) for each sequence in the input file.
+
+
+]]>
+    </help>
+    <expand macro="requirements" />
+</tool>