Mercurial > repos > rnateam > viennarna_rnasnoop
diff rnasnoop.xml @ 0:c4a5139922f6 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
author | rnateam |
---|---|
date | Tue, 06 Dec 2016 12:36:54 -0500 |
parents | |
children |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rnasnoop.xml Tue Dec 06 12:36:54 2016 -0500 @@ -0,0 +1,138 @@ +<tool id="viennarna_rnasnoop" name="@EXECUTABLE@" version="@VERSION@.0"> + <description> Find targets of a query H/ACA snoRNA</description> + + <macros> + <token name="@EXECUTABLE@">RNAsnoop</token> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <expand macro="stdio" /> + <expand macro="version_command" /> + <command> +<![CDATA[ + RNAsnoop --query='$input1' --target='$input2' > '$output' + --alignmentLength=$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" 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> + <when value="basic"> + </when> + </conditional> + </inputs> + <outputs> + <data format="txt" name="output"/> + <data format="tar" name="imagesFile"> + <filter>filetypeOptions['filetypeSelector'] == "fasta"</filter> + </data> + + </outputs> + <tests> + <test> + <param name="input1" value="rnasnoop_input1b.fa"/> + <param name="input2" value="rnasnoop_input1a.fa"/> + <output name="output" file="rnasnoop_result1.txt"/> + </test> + </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="citations" /> +</tool>