diff rnasnoop.xml @ 0:78d673470d45 draft

Imported from capsule None

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rnasnoop.xml	Wed Feb 04 12:05:27 2015 -0500
@@ -0,0 +1,131 @@
+<tool id="rnasnoop" name="RNAsnoop" version="2.1.6.0">
+    <description> Find targets of a query H/ACA snoRNA</description>
+    <expand macro="requirements" />
+    <expand macro="version_command" />
+    <expand macro="stdio" />
+    <macros>
+        <token name="@EXECUTABLE@">RNAsnoop</token>
+        <import>macros.xml</import>
+    </macros>
+    <command>
+<![CDATA[
+        RNAsnoop --query=$input1 --target=$input2 > $output
+        --alignmentLenght=$length
+        $constraint
+        --energy-threshold=$energyThreshold
+        #if $varExists('$advancedOptions.extensioncost')
+            $advancedOptions.fast
+            --extension-cost=$advancedOptions.extensioncost
+            --minimal-right-duplex=$advancedOptions.minrightduplex
+            --minimal-loop-energy=$advancedOptions.minloop
+            --minimal-left-duplex=$advancedOptions.minleftduplex
+            --minimal-duplex=$advancedOptions.minduplex
+            --duplex-distance=$advancedOptions.duplexdist
+            --minimal-stem-length=$advancedOptions.minstemlength
+            --maximal-stem-length=$advancedOptions.maxstemlength
+            --minimal-duplex-box-length=$advancedOptions.minbox
+            --maximal-duplex-box-length=$advancedOptions.maxbox
+            --minimal-snoRNA-stem-loop-length=$advancedOptions.minsnornastem
+            --maximal-snoRNA-stem-loop-length=$advancedOptions.maxsnornastem
+            --minimal-snoRNA-duplex-length=$advancedOptions.minsnornaduplex
+            --maximal-snoRNA-duplex-length=$advancedOptions.maxsnornaduplex
+            --minimal-duplex-stem-energy=$advancedOptions.minduplexstem
+            --minimal-total-energy=$advancedOptions.mintotal
+            --maximal-stem-asymmetry=$advancedOptions.maxstemasymmetry
+            --minimal-lower-stem-energy=$advancedOptions.minstemenergy
+        #end if
+        #if $filetypeOptions.filetypeSelector == "fasta"
+            ; tar -cf $imagesFile *.ps
+        #else
+            --alignment-mode
+        #end if
+]]>
+    </command>
+
+    <inputs>
+        <conditional name="filetypeOptions">
+            <param name="filetypeSelector" type="select" label="Select Filetype">
+                <option value="fasta" selected="true">Fasta</option>
+                <option value="clustal">Clustal</option>
+            </param>
+            <when value="fasta">
+                <param format="fasta" name="input1" type="data" label="Query sequences"/>
+                <param format="fasta" name="input2" type="data" label="Target sequences"/>
+            </when>
+            <when value="clustal">
+                <param format="txt" name="input1" type="data" label="Query sequences"/>
+                <param format="txt" name="input2" type="data" label="Target sequences"/>
+            </when>
+        </conditional>
+
+
+        <param name="length" type="integer" min="0" value="25" label="Maximal alignment length" help="--alignmentLength"/>
+        <param name="constraint" type="boolean" truevalue="--constraint" falsevalue="" checked="false" label="Calculate the stem structure subject to constraints" help="--constraint"/>
+        <param name="energyThreshold" size="8" type="float" value="-1.0" label="Maximal energy difference between the mfe and the desired suboptimal structure" help="--energy-threshold"/>
+
+        <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="fast" type="boolean" truevalue="--fast-folding=1" falsevalue="--fast-folding=0" checked="true" label="Backtracking based on the standard energy model" help="--fast-folding"/>
+                <param name="extensioncost" type="integer" value="0" label="Cost to add each nucleotide in a duplex" help="--extension-cost"/>
+                <param name="minrightduplex" type="integer" value="-270" label="Minimal right duplex energy" help="--minimal-right-duplex"/>
+                <param name="minloop" type="integer" value="-280" label="Minimal Loop energy" help="--minimal-loop-energy"/>
+                <param name="minleftduplex" type="integer" value="-170" label="Minimal left duplex energy" help="--minimal-left-duplex"/>
+                <param name="minduplex" type="integer" value="-1090" label="Minimal duplex energy" help="--minimal-duplex"/>
+                <param name="duplexdist" type="integer" value="2" label="Distance between target 3' ends of two consecutive duplexes" help="--duplex-distance"/>
+                <param name="minstemlength" type="integer" value="5" label="Minimal snoRNA stem length" help="--minimal-stem-length"/>
+                <param name="maxstemlength" type="integer" value="120" label="Maximal snoRNA stem length" help="--maximal-stem-length"/>
+                <param name="minbox" type="integer" value="11" label="Minimal distance between the duplex end and the H/ACA box" help="--minimal-duplex-box-length"/>
+                <param name="maxbox" type="integer" value="16" label="Maximal distance between the duplex end and the H/ACA box" help="--maximal-duplex-box-length"/>
+                <param name="minsnornastem" type="integer" value="1" label="Minimal distance between the stem loop and the snoRNA sequence" help="--minimal-snoRNA-stem-loop-length"/>
+                <param name="maxsnornastem" type="integer" value="100000" label="Maximal distance between the stem loop and the snoRNA sequence" help="--maximal-snoRNA-stem-loop-length"/>
+                <param name="minsnornaduplex" type="integer" value="0" label="Minimal distance between the duplex and the snoRNA sequence" help="--minimal-snoRNA-duplex-length"/>
+                <param name="maxsnornaduplex" type="integer" value="0" label="Maximal distance between the duplex and the snoRNA sequence" help="--maximal-snoRNA-duplex-length"/>
+                <param name="minduplexstem" type="integer" value="-1370" label="Minimal duplex stem energy" help="--minimal-duplex-stem-energy"/>
+                <param name="mintotal" type="integer" value="100000" label="Minimal total energy" help="--minimal-total-energy"/>
+                <param name="maxstemasymmetry" type="integer" value="30" label="Maximal snoRNA stem asymmetry" help="--maximal-stem-asymmetry"/>
+                <param name="minstemenergy" type="integer" value="100000" label="Minimal lower stem energy" help="--minimal-lower-stem-energy"/>
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data format="txt" name="output"/>
+        <data format="tar" name="imagesFile">
+             <filter>filetypeOptions['filetypeSelector'] == "fasta"</filter>
+        </data>
+
+    </outputs>
+    <tests>
+    </tests>
+    <help>
+<![CDATA[
+
+**RNAsnoop**
+
+reads a target RNA sequence and a H/ACA snoRNA sequence from a target and query file, respectively and computes optimal and suboptimal secondary structures for their hybridization. The calculation can be done roughly done in O(nm), where is n the length of the target sequence and m is the length of the snoRNA stem, as it is specially tailored to the special case of H/ACA snoRNA. For general purpose target predictions, please have a look at RNAduplex, RNAup, RNAcofold and RNAplex.
+
+
+-----
+
+**Input format**
+
+RNAsnoop requires two input files
+
+- either two Fasta files
+- or two Clustal alignment files
+
+------
+
+**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 '<>' brackets represent snoRNA intramolecular interactions, while the '()' brackets represent intermolecular interactions between the snoRNA and its target.
+The range of the structure in the two sequences in the format "from,to : from,to"; the energy of duplex structure in kcal/mol. If available the opening energy are also returned.
+
+
+]]>
+    </help>
+    <expand macro="requirements" />
+</tool>