diff rnaaliduplex.xml @ 0:78d673470d45 draft

Imported from capsule None

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaaliduplex.xml	Wed Feb 04 12:05:27 2015 -0500
@@ -0,0 +1,92 @@
+<tool id="rnaaliduplex" name="RNAaliduplex" version="2.1.6.0">
+    <description>find binding sites of two RNA alignments</description>
+    <expand macro="requirements" />
+    <expand macro="version_command" />
+    <expand macro="stdio" />
+    <macros>
+        <token name="@EXECUTABLE@">RNAaliduplex</token>
+        <import>macros.xml</import>
+    </macros>
+    <command>
+<![CDATA[
+        RNAaliduplex -T $temperature -d $dangling $flagsort --deltaEnergy=$deltaenergy $input1 $input2
+        #if $varExists('$advancedOptions.noconversion')
+            $advancedOptions.noconversion
+            $advancedOptions.gquad
+            $advancedOptions.nolp
+            $advancedOptions.nogu
+            $advancedOptions.noclosinggu
+            $advancedOptions.notetra
+        #end if
+        > $out_file
+]]>
+    </command>
+    <inputs>
+        <param format="txt" name="input1" type="data" label="Clustal alignment file"/>
+        <param format="txt" name="input2" type="data" label="Clustal alignment file"/>
+        <param name="temperature" size="6" type="float" value="37.0" label="Temperature [°C]" help="-T"/>
+        <param name="deltaenergy" size="6" type="float" value="0.0" label="Compute suboptimal structures with an maximal energy difference [kcal/mol] to optimum" help="--deltaEnergy=range"/>
+        <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="flagsort" type="boolean" checked="false" label="Output will be sorted by free energy" truevalue="--sorted" falsevalue="" help="--sorted"/>
+        <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" checked="false" truevalue="--noconv" falsevalue="" label="no conversion" help="--noconv  do not convert thymine to uracile (T -> U)."/>
+                <param name="nogu" type="boolean" checked="false" truevalue="-noGU" falsevalue="" label="No GU pairing" help="--noGU  don't allow pairing of G and U."/>
+                <param name="noclosinggu" type="boolean" checked="false" truevalue="--noClosingGU" falsevalue="" 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" truevalue="--noTetra" falsevalue="" label="No stabilization for loops, hairpins etc." help="--noTetra"/>
+                <param name="nolp" type="boolean" checked="false" truevalue="--noLP" falsevalue="" label="No lonely pairs (helices of length 1) will be created." help="--noLP"/>
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data format="txt" name="out_file"/>
+    </outputs>
+    <tests>
+    </tests>
+    <help>
+<![CDATA[
+**RNAaliduplex**
+
+The program reads two alignments of RNA sequences in CLUSTAL format and
+predicts optimal and suboptimal binding sites, hybridization energies and the
+corresponding structures. The calculation takes only inter-molecular base pairs
+into account, for the general case use RNAcofold. The use of alignments allows
+to focus on binding sites that are evolutionary conserved. Note, that the two
+input alignments need to have an equal number of sequences and the same order,
+i.e. the 1st sequence in file1 will be hybridized to the 1st in file2 etc.
+
+The computed binding sites, energies, and structures are written to stdout, one
+structure per line. Each line consist of: The structure in dot bracket format
+with a &  separating the two strands. The range of the structure in the two
+sequences in the format  "from,to : from,to"; the energy of duplex structure
+in kcal/mol.
+The format is especially useful for computing the hybrid structure between a
+small probe sequence and a long target sequence.
+
+
+
+-----
+
+**Input format**
+
+RNAaliduplex takes two alignment files generated with Clustal (*.aln).
+
+------
+
+**Outputs**
+
+- text output with several secondary structures and its energies
+
+]]>
+    </help>
+    <expand macro="requirements" />
+</tool>