diff rna2dfold.xml @ 0:78d673470d45 draft

Imported from capsule None

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rna2dfold.xml	Wed Feb 04 12:05:27 2015 -0500
@@ -0,0 +1,115 @@
+<tool id="rna2dfold" name="RNA2Dfold" version="2.1.6.0">
+    <description>explore structure space between two reference structures</description>
+    <expand macro="requirements" />
+    <expand macro="version_command" />
+    <expand macro="stdio" />
+    <macros>
+        <token name="@EXECUTABLE@">RNA2Dfold</token>
+        <import>macros.xml</import>
+    </macros>
+    <command>
+<![CDATA[
+        RNA2Dfold -T $temperature -d $dangling --stochBT=$nrbt
+        #if int($nk) > -1 and int($nl) > -1
+            --neighborhood=$nk:$nl
+        #end if
+        #if $varExists('$pfselect.pfscaling')
+            --partfunc --pfScale=$pfselect.pfscaling
+        #end if
+        #if $varExists('$advancedOptions.noconversion')
+            #if $advancedOptions.noconversion
+                --noconv
+            #end if
+            #if $advancedOptions.nogu
+                --noGU
+            #end if
+            #if $advancedOptions.noclosinggu
+                --noClosingGU
+            #end if
+            #if $advancedOptions.notetra
+                --noTetra
+            #end if
+            --maxDist1=$maxK
+            --maxDist2=$maxL
+        #end if
+        < $custom_input > $out_file
+]]>
+    </command>
+    <inputs>
+        <param format="txt" name="custom_input" type="data" label="Custom File"/>
+        <param name="temperature" size="6" type="float" value="37.0" label="Temperature [°C]" help="-T"/>
+        <param name="nrbt" type="integer" value="1" label="number of backtrack of Boltzmann samples" help="--stochBT=INT"/>
+        <param name="nk" type="integer" value="-1" label="k distance to first reference structure of neighborhood in which to backtrack" help="--neighborhood=k:l"/>
+        <param name="nl" type="integer" value="-1" label="l distance to second reference structure of neighborhood in which to backtrack" help="--neighborhood=k:l"/>
+        <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="circular" type="boolean" checked="false" label="assume circular RNA structure" help="--circ"/>
+        <conditional name="pfselect">
+            <param name="pf" type="select" label="calculate partition function" help="--partfunc">
+                <option value="no">no</option>
+                <option value="yes">yes</option>
+            </param>
+            <when value="yes">
+                <param name="pfscaling" size="6" type="float" value="1.0" label="scaling factor for the partition function"/>
+            </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="maxK" type="integer" value="50" label="Maximum distance to first reference structure" help="--maxDist1=INT"/>
+                <param name="maxL" type="integer" value="50" label="Maximum distance to second reference structure" help="--maxDist2=INT"/>
+                <param name="noconversion" type="boolean" checked="false" label="no conversion" help="--noconv  do not convert thymine to uracile (T -> U)."/>
+                <param name="gquad" type="boolean" checked="false" label="G Quadruplex formation" help="-g  take into account G Quadruplex formation"/>
+                <param name="nogu" type="boolean" checked="false" label="No GU pairing" help="--noGU  don't allow pairing of G and U."/>
+                <param name="noclosinggu" type="boolean" 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" checked="false" label="No stabilization for loops, hairpins etc." help="--noTetra"/>
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data format="txt" name="out_file"/>
+    </outputs>
+    <tests>
+    </tests>
+    <help>
+<![CDATA[
+**RNA2Dfold**
+
+The program partitions the secondary structure space into (basepair)distance
+classes according to two fixed reference structures. It expects a sequence and
+two secondary structures in dot-bracket notation as its inputs. For each
+distance class, the MFE representative, Boltzmann probabilities and Gibbs free
+energy is computed. Additionally, a stochastic backtracking routine allows to
+produce samples of representative suboptimal secondary structures from each
+partition.
+The k-distance corresponds to the distance to the first reference structure, and
+the l-distance corresponds to the distance to the second reference structure
+
+-----
+
+**Input format**
+
+RNA2Dfold requires one input file in the following format
+
+- 1st line: RNA sequence
+- 2nd line: first reference structure in dot-bracket format
+- 3rd line: second reference structure in dot-bracket format
+
+------
+
+**Outputs**
+
+- text output with several secondary structures and its energies
+
+]]>
+    </help>
+    <expand macro="requirements" />
+</tool>