diff rnaplex.xml @ 0:78d673470d45 draft

Imported from capsule None

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaplex.xml	Wed Feb 04 12:05:27 2015 -0500
@@ -0,0 +1,126 @@
+<tool id="rnaplex" name="RNAplex" version="2.1.6.0">
+    <description>Find targets of a query RNA</description>
+    <expand macro="requirements" />
+    <expand macro="version_command" />
+    <expand macro="stdio" />
+    <macros>
+        <token name="@EXECUTABLE@">RNAplex</token>
+        <import>macros.xml</import>
+    </macros>
+    <command>
+<![CDATA[
+        RNAplex
+        #if str($clustalOption.clustalFlag) == "clustal"
+            --alignment-mode
+            -q$input1 -t$input2
+        #else
+            < $input
+        #end if
+        -T$temperature
+        --interaction-length=$maxLength
+        --extension-cost=$extensionCost
+        --scale-accessibility=$scaleAccessibility
+        $constraint
+
+
+        #if $varExists('clustalOption.meltingOption.probeConc')
+            --probe-mode
+            --probe-concentration=$clustalOption.meltingOption.probeConc
+            --na-concentration=$clustalOption.meltingOption.naConc
+            --mg-concentration=$clustalOption.meltingOption.mgConc
+            --k-concentration=$clustalOption.meltingOption.kConc
+            --tris-concentration=$clustalOption.meltingOption.trisConc
+        #end if
+
+
+
+        #if $varExists('$advancedOptions.duplexDistance')
+            --fast-folding=$advancedOptions.fastFolding
+            --duplex-distance=$advancedOptions.duplexDistance
+            --energy-threshold=$advancedOptions.enThreshold
+        #end if
+        > $output
+]]>
+    </command>
+
+    <inputs>
+    <conditional name="clustalOption">
+        <param name="clustalFlag" type="select" label="Input options">
+            <option value="fasta" selected="true">Fasta input file</option>
+            <option value="clustal">Clustalw input files</option>
+        </param>
+        <when value="fasta">
+            <param format="fasta" name="input" type="data" label="Fasta file"/>
+            <conditional name="meltingOption">
+                <param name="meltingSelector" type="select" label="calculate melting temperature">
+                    <option value="no" selected="true">no</option>
+                    <option value="yes">yes</option>
+                </param>
+                <when value="yes">
+                    <param name="probeConc" type="float" value="0.1" label="Concentration of the probe" help="--probe-concentration"/>
+                    <param name="naConc" type="float" value="1.0" label="Na concentration" help="--na-concentration"/>
+                    <param name="mgConc" type="float" value="1.0" label="Mg concentration" help="--mg-concentration"/>
+                    <param name="kConc" type="float" value="1.0" label="K concentration" help="--k-concentration"/>
+                    <param name="trisConc" type="float" value="1.0" label="Tris concentration" help="--tris-concentration"/>
+                </when>
+            </conditional>
+            </when>
+        <when value="clustal">
+            <param format="txt" name="input1" type="data" label="Clustal file / Query sequences"/>
+            <param format="txt" name="input2" type="data" label="Clustal file / Target sequences"/>
+        </when>
+    </conditional>
+        <param name="temperature" size="8" type="float" value="37.0" label="temperature [°C]" help="-T"/>
+        <param name="maxLength" type="integer" min="0" value="40" label="maximal interaction length" help="--interaction-length"/>
+        <param name="extensionCost" type="integer" value="0" label="extension cost" help="--extension-cost"/>
+        <param name="extensionCost" type="integer" value="0" label="extension cost" help="--extension-cost"/>
+        <param name="scaleAccessibility" size="8" type="float" value="1.0" label="scale all opening energy by a factor" help="--scale-accessibility"/>
+        <param name="constraint" type="boolean" truevalue="--constraint" falsevalue="" checked="false" label="Calculate structures subject to constraints. Constraints have to be given in the input file" help="--constraint"/>
+
+
+        <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="fastFolding" type="select" label="Backtracking" help="--fast-folding">
+                    <option value="0" selected="true">based on standard energy model (0) - normal</option>
+                    <option value="2">based on approximate plex model (2) - faster</option>
+                    <option value="1">no recomputation (1) - fastest</option>
+                </param>
+                <param name="duplexDistance" type="integer" value="0" label="Distance between target 3' ends of two consecutive duplexes" help="--duplex-distance"/>
+                <param name="enThreshold" size="8" type="float" value="-100000" label="Minimum Energy Gain for a Duplex [kcal/mol]" help="--energy-threshold"/>
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data format="txt" name="output"/>
+    </outputs>
+    <tests>
+    </tests>
+    <help>
+<![CDATA[
+
+**RNAplex**
+
+Computes optimal and suboptimal secondary structures for their hybridization. The calculation is simplified by allowing only inter-molecular base pairs.
+
+
+-----
+
+**Input format**
+
+RNALplex requires either one Fasta file or two Clustal files as input
+
+------
+
+**Outputs**
+
+The computed optimal and suboptimal structure are given, 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.
+
+
+]]>
+    </help>
+    <expand macro="requirements" />
+</tool>