diff rna2dfold.xml @ 0:0373277da3ec draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rna2dfold.xml	Tue Dec 06 12:36:38 2016 -0500
@@ -0,0 +1,108 @@
+<tool id="viennarna_rna2dfold" name="@EXECUTABLE@" version="@VERSION@.0">
+    <description>explore structure space between two reference structures</description>
+    <macros>
+        <token name="@EXECUTABLE@">RNA2Dfold</token>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="stdio" />
+    <expand macro="version_command" />
+    <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
+        $noBT
+        $advancedOptions.noconversion
+        $advancedOptions.noclosinggu
+        $advancedOptions.notetra
+        $advancedOptions.circ
+        #if $varExists('$advancedOptions.maxK')    
+            --maxDist1=$advancedOptions.maxK
+            --maxDist2=$advancedOptions.maxL
+        #end if
+        < '$custom_input' > '$out_file'
+]]>
+    </command>
+    <inputs>
+        <param format="txt,dbn" name="custom_input" type="data" label="Custom File"/>
+        <param name="temperature" 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>
+        </param>
+        <param name="noBT" type="boolean" checked="true" truevalue="" falsevalue="--noBT" 
+            label="Backtrack structures, don't calculate energy contributions only" argument="--noBT"/>
+        <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" type="float" value="1.0" label="Scaling factor for the partition function"/>
+            </when>
+            <when value="no">
+            </when>
+        </conditional>
+        <section name="advancedOptions" title="Advanced options">
+            <param name="noclosinggu" type="boolean" truevalue="" falsevalue="--noClosingGU" checked="true" label="Allow GU pairing at the ends" help="Allow pairing of G and U at the ends of helices. --noClosingGU"/>
+            <param name="noconversion" type="boolean" truevalue="" falsevalue="--noconv" checked="true" label="Convert Thymine to Uracil (T -> U)" help="Avoids confusion with DNA sequences (--noconv)"/>
+            <param name="notetra" type="boolean" truevalue="" falsevalue="--noTetra" checked="true" label="Allow stabilization for loops, hairpins etc." help=" Include special tabulated stabilizing energies for tri-, tetra- and hexaloop hairpins. Mostly for testing. (--noTetra)"/>                
+            <param argument="--circ" type="boolean" truevalue="--circ" falsevalue="" checked="false" label="Model as circular RNA structure"/>                                      
+            <param name="maxK" type="integer" value="10" max="44" label="Maximum distance to first reference structure" argument="--maxDist1"/>
+            <param name="maxL" type="integer" value="10" max="43" label="Maximum distance to second reference structure" argument="--maxDist2"/>
+            <!-- This argument causes "Segmentation fault"-->
+            <!-- <param name="nogu" type="boolean" truevalue="" falsevalue="- -noGU" checked="true" label="Allow GU pairing" help="Allow wobbly pairs G-U."/> -->               
+        </section>
+    </inputs>
+    <outputs>
+        <data format="dbn" name="out_file"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="custom_input" value="rna2dfold_input1.txt"/>
+            <param name="nrbt" value="0"/>
+            <output name="out_file1" file="rna2dfold_result1.txt"/>
+        </test>
+    </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="citations" />
+</tool>