diff rnaaliduplex.xml @ 0:d4f6c7ba5f69 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/rnaaliduplex.xml	Tue Dec 06 12:36:05 2016 -0500
@@ -0,0 +1,96 @@
+<tool id="viennarna_rnaaliduplex" name="@EXECUTABLE@" version="@VERSION@.0">
+    <description>find binding sites of two RNA alignments</description>
+    <macros>
+        <token name="@EXECUTABLE@">RNAaliduplex</token>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="stdio" />
+    <expand macro="version_command" />
+    <command>
+<![CDATA[
+        RNAaliduplex -T $temperature -d $dangling $flagsort --deltaEnergy=$deltaEnergy '$input1' '$input2'
+        $advancedOptions.noconversion
+        $advancedOptions.nolp
+        $advancedOptions.nogu
+        $advancedOptions.noclosinggu
+        $advancedOptions.notetra
+        #if $advancedOptions.nsp
+            --nsp='$advancedOptions.nsp'
+        #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" type="float" value="37.0" label="Temperature [°C]" help="-T"/>
+        <param argument="--deltaEnergy" type="float" value="0.0" label="Compute suboptimal structures with energy in a certain range of the optimum [kcal/mol]" 
+            help="Default is calculation of mfe structure only."/>
+        <param name="dangling" type="select" label="How to treat dangling end energiesHow to treat dangling end energies for bases adjacent to helices in free ends and multi-loops" argument="-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="flagsort" type="boolean" checked="false" label="Output will be sorted by free energy" truevalue="--sorted" falsevalue="" help="--sorted"/>
+        <section name="advancedOptions" title="Advanced options">
+            <param name="nolp" type="boolean" truevalue="" falsevalue="--noLP" checked="true" label="Allow lonely base-pairs" help="(--noLP)"/>
+            <param name="nogu" type="boolean" truevalue="" falsevalue="--noGU" checked="true" label="Allow GU pairing" help="--noGU"/>
+            <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 name="nsp" type="text" value="" label="Allow other pairs in addition to the usual AU,GC,and GU pairs." 
+                help="Its argument is a comma separated list of additionally allowed pairs. If the first character is '-' then AB will imply that AB and BA are allowed pairs. e.g. RNAfold -nsp -GA  will allow GA and AG pairs. Nonstandard pairs are given 0 stacking energy." 
+                argument="--nsp"/>
+        </section>
+    </inputs>
+    <outputs>
+        <data format="dbn" name="out_file"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input1" value="rnaaliduplex_input1.clustal"/>
+            <param name="input2" value="rnaaliduplex_input1.clustal"/>
+            <output name="out_file1" file="rnaaliduplex_result1.txt"/>
+        </test>
+    </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="citations" />
+</tool>