diff rnaplfold.xml @ 0:78d673470d45 draft

Imported from capsule None

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaplfold.xml	Wed Feb 04 12:05:27 2015 -0500
@@ -0,0 +1,110 @@
+<tool id="rnaplfold" name="RNAplfold" version="2.1.6.0">
+    <description> predicts RNA secondary structures including pseudoknots</description>
+    <expand macro="requirements" />
+    <expand macro="version_command" />
+    <expand macro="stdio" />
+    <macros>
+        <token name="@EXECUTABLE@">RNAplfold</token>
+        <import>macros.xml</import>
+    </macros>
+    <command>
+<![CDATA[
+        RNAplfold < $input
+        -T$temperature
+        --dangles=$dangling
+        --cutoff=$cutoff
+        --winsize=$winsize
+        --span=$span
+        $onthefly
+        $openingenergies
+        #if $varExists('$unpairedOption.ulength')
+            --ulength=$unpairedOption.ulength
+        #end if
+
+        #if $varExists('$advancedOptions.nolp')
+            $advancedOptions.noconv
+            $advancedOptions.nolp
+            $advancedOptions.nogu
+            $advancedOptions.noclosinggu
+            $advancedOptions.notetra
+        #end if
+        ;ls *_basepairs *_lunp *_openen > files.tmp
+        ;tar -cf $outputf --files-from=files.tmp
+
+]]>
+    </command>
+
+    <inputs>
+        <param format="fasta" name="input" type="data" label="Fasta file"/>
+        <param name="temperature" size="8" 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="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="winsize" type="integer" value="70" label="Average pairing probabilities over this windowsize" help="--winsize"/>
+        <param name="span" type="integer" value="70" label="Maximum seperation between base pairs" help="--span, -L"/>
+        <param name="cutoff" size="8" type="float" value="0.01" label="Cutoff probability for report on base pairing" help="--cutoff"/>
+        <param name="onthefly" type="boolean" truevalue="--print_onthefly" falsevalue="" checked="false" label="Print simplified base pair probabilities (_basepairs output)" help="--print_onthefly"/>
+        <param name="openingenergies" type="boolean" truevalue="--opening_energies" falsevalue="" checked="false" label="Output in logarithm of the probabilities (_openen output)" help="--opening_energies"/>
+        <conditional name="unpairedOption">
+            <param name="unpairedSelector" type="select" label="Compute probabilty that region is unpaired (_lunp output)">
+                <option value="no" selected="true">no</option>
+                <option value="yes">yes</option>
+            </param>
+            <when value="yes">
+                <param name="ulength" type="integer" value="31" label="Maximal lenght of unpaired region" help="--ulength"/>
+            </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="noconv" type="boolean" truevalue="--noconv" falsevalue="" checked="false" label="No conversion of T -> U" help="--noconv"/>
+                <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"/>
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <collection name="matrix_outputs" type="list" label="rna_eps outputs">
+            <discover_datasets pattern="(?P&lt;designation&gt;.+)_dp\.ps" ext="rna_eps" visible="true"/>
+        </collection>
+        <data format="tar" name="outputf"/>
+    </outputs>
+    <tests>
+    </tests>
+    <help>
+<![CDATA[
+
+**RNAplfold**
+
+Computes local pair probabilities for base pairs with a maximal span of L. The probabilities are averaged over all windows of size L that contain the base pair. For a sequence of length n and a window size of L the algorithm uses only O(n+L*L) memory and O(n*L*L) CPU time. Thus it is practical to "scan" very large genomes for short stable RNA structures.
+
+
+-----
+
+**Input format**
+
+RNAPplfold requires one input file
+
+- Fasta file
+
+------
+
+**Outputs**
+
+For each structure in the Fasta input a postscript image with dot-plot of the pairing probabilities is generated. Different output is generated with the "--ulength", "--print_onthefly" and "--opening_energies" flags.
+The Dot Plot Matrices are stored in a Postscript file.
+The other output is packed in a tar file.
+
+
+]]>
+    </help>
+    <expand macro="requirements" />
+</tool>