Mercurial > repos > rnateam > viennarna_rnaplex
diff rnaplex.xml @ 0:283a7479bd3f 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 12:32:55 -0500 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rnaplex.xml Tue Dec 06 12:32:55 2016 -0500 @@ -0,0 +1,130 @@ +<tool id="viennarna_rnaplex" name="@EXECUTABLE@" version="@VERSION@.0"> + <description>Find targets of a query RNA</description> + + <macros> + <token name="@EXECUTABLE@">RNAplex</token> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <expand macro="stdio" /> + <expand macro="version_command" /> + <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> + <when value="no"> + </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" 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" 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" type="float" value="-100000" label="Minimum Energy Gain for a Duplex [kcal/mol]" help="--energy-threshold"/> + </when> + <when value="basic"> + </when> + </conditional> + </inputs> + <outputs> + <data format="txt" name="output"/> + </outputs> + <tests> + <test> + <param name="input" value="rnaplex_input1.fa"/> + <output name="out_file" file="rnaplex_result1.txt"/> + </test> + </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="citations" /> +</tool>