diff rnacofold.xml @ 0:78d673470d45 draft

Imported from capsule None

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rnacofold.xml	Wed Feb 04 12:05:27 2015 -0500
@@ -0,0 +1,93 @@
+<tool id="rnacofold" name="RNAcofold" version="2.1.6.0">
+    <description>Calculate secondary structures of two RNAs with dimerization</description>
+    <expand macro="requirements" />
+    <expand macro="version_command" />
+    <expand macro="stdio" />
+    <macros>
+        <token name="@EXECUTABLE@">RNAcofold</token>
+        <import>macros.xml</import>
+    </macros>
+    <command>
+<![CDATA[
+        RNAcofold  < $input > $tabularFile
+        -T$temperature -d$dangling
+        $pf
+        $allpf
+        #if $varExists('$advancedOptions.noconversion')
+            $advancedOptions.constraint
+            $advancedOptions.noconversion
+            $advancedOptions.gquad
+            $advancedOptions.nolp
+            $advancedOptions.nogu
+            $advancedOptions.noclosinggu
+            $advancedOptions.notetra
+        #end if
+]]>
+    </command>
+    <inputs>
+        <param format="fasta" name="input" type="data" label="Fasta file"/>
+        <param name="temperature" size="6" 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="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="pf" type="boolean" checked="false" truevalue="--partfunc" falsevalue="" label="Calculate Partition Function" help="--partfunc"/>
+        <param name="allpf" type="boolean" checked="false" truevalue="--all_pf" falsevalue="" label="Calculate homo-dimers" help="--all_pf"/>
+        <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="constraint" type="boolean" truevalue="--constraint" falsevalue="" checked="false" label="Calculate structure subject to constraints" help="--constraint"/>
+                <param name="noconversion" type="boolean" truevalue="--noconv" falsevalue="" checked="false" label="No conversion T->U" help="--noconv"/>
+                <param name="gquad" type="boolean" truevalue="--gquad" falsevalue="" checked="false" label="G Quadruplex formation" help="-g  take into account G Quadruplex formation"/>
+                <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>
+        <data format="txt" name="tabularFile"/>
+        <collection name="sequence_outputs" type="list" label="rna_eps outputs">
+            <discover_datasets pattern="(?P&lt;designation&gt;.+)_ss\.ps" ext="eps" />
+        </collection>
+        <collection name="matrix_outputs" type="list" label="rna_eps outputs">
+            <filter>pf is True</filter>
+            <discover_datasets pattern="(?P&lt;designation&gt;.+)_dp\.ps" ext="rna_eps" visible="true"/>
+        </collection>
+    </outputs>
+    <tests>
+    </tests>
+    <help>
+<![CDATA[
+**RNAcofold**
+
+
+-----
+
+**Input format**
+
+RNAcofold requires one input file:
+
+- Fasta file
+
+Two different RNA sequences can be specified concatenated with the '&' character. The folding of the two sequences with each other will be calculated.
+
+
+------
+
+**Outputs**
+
+- Energies of the RNA sequences and the dimers
+- Structure images
+- Dot Plot Matrix images (if --partfunc is used)
+
+]]>
+    </help>
+    <expand macro="requirements" />
+</tool>