diff rnaalifold.xml @ 0:78d673470d45 draft

Imported from capsule None

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaalifold.xml	Wed Feb 04 12:05:27 2015 -0500
@@ -0,0 +1,119 @@
+<tool id="rnaalifold" name="RNAalifold" version="2.1.6.0">
+    <description>Calculate minimum free energy secondary structures and partition function on a multiple alignment file</description>
+    <expand macro="requirements" />
+    <expand macro="version_command" />
+    <expand macro="stdio" />
+    <macros>
+        <token name="@EXECUTABLE@">RNAalifold</token>
+        <import>macros.xml</import>
+    </macros>
+    <command>
+<![CDATA[
+        RNAalifold  < $input > $tabularFile
+        -T$temperature -d$dangling
+        $pf
+        $mis
+        #if $measelect.mea=="yes"
+            --mea=$measelect.meavalue
+        #end if
+        #if $backtrackselect.backtrack=="yes"
+            --stochBT_en=$backtrackselect.backtrackvalue
+        #end if
+        #if $varExists('$advancedOptions.color')
+            $advancedOptions.alignment
+            $advancedOptions.color
+            $advancedOptions.gquad
+            $advancedOptions.nolp
+            $advancedOptions.nogu
+            $advancedOptions.noclosinggu
+            $advancedOptions.notetra
+            $advancedOptions.canonicalonly
+            $advancedOptions.circular
+            --cfactor=$advancedOptions.cfactor
+            --nfactor=$advancedOptions.nfactor
+            $advancedOptions.endgaps
+            $advancedOptions.ribosum
+        #end if
+        ; tar -cf $imagesFile *.ps
+]]>
+    </command>
+    <inputs>
+        <param format="clustal" name="input" type="data" label="Clustal 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>
+        <param name="pf" type="boolean" checked="false" truevalue="-p" falsevalue="" label="calculate partition function" help="-p"/>
+        <param name="mis" type="boolean" checked="false" truevalue="--mis" falsevalue="" label="Most Informative Sequence" help="--mis"/>
+        <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>
+        </conditional>
+        <conditional name="backtrackselect">
+            <param name="backtrack" type="select" label="number of structures" help="--stochBT_en">
+                <option value="no">no</option>
+                <option value="yes">yes</option>
+            </param>
+            <when value="yes">
+                <param name="backtrackvalue" size="4" type="integer" value="1" label="Number of random structures."/>
+            </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="alignment" type="boolean" truevalue="--aln" falsevalue="" checked="false" label="Colored and annotated alignment image" help="--color"/>
+                <param name="color" type="boolean" truevalue="--color" falsevalue="" checked="false" label="Colored secondary structure image" help="--color"/>
+                <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"/>
+                <param name="cfactor" size="6" type="float" value="1.0" label="Weight of the covariance term" help="--cfactor"/>
+                <param name="nfactor" size="6" type="float" value="1.0" label="Penalty for non-compatible sequences in the covariance term" help="--nfactor"/>
+                <param name="endgaps" type="boolean" truevalue="--endgaps" falsevalue="" checked="false" label="Score pairs with endgaps same as gap-gap pairs" help="--endgaps"/>
+                <param name="ribosum" type="boolean" truevalue="--ribosum_scoring" falsevalue="" checked="false" label="Use ribosum scoring matrix" help="--ribosum_scoring"/>
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data format="txt" name="tabularFile"/>
+        <data format="tar" name="imagesFile"/>
+    </outputs>
+    <tests>
+    </tests>
+    <help>
+<![CDATA[
+**RNAalifold**
+
+-----
+
+**Input format**
+
+RNAalifold requires one input file
+- Clustal file
+
+------
+
+**Outputs**
+
+- energy of the consensus structures in the clustal file
+- several possible postscript images bundled together in a tar file
+
+
+]]>
+    </help>
+    <expand macro="requirements" />
+</tool>