annotate rnaeval.xml @ 2:5e58cbf27a05 draft

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author rnateam
date Mon, 09 Feb 2015 13:26:11 -0500
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1 <tool id="rnaeval" name="RNAeval" version="2.1.6.0">
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2 <description>Calculate energy of RNA sequences with given secondary structure</description>
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3 <expand macro="requirements" />
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4 <expand macro="version_command" />
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5 <expand macro="stdio" />
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6 <macros>
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7 <token name="@EXECUTABLE@">RNAeval</token>
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8 <import>macros.xml</import>
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9 </macros>
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10 <command>
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11 <![CDATA[
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12 RNAeval < $input > $tabularFile
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13 -T$temperature -d$dangling
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14 #if $varExists('$advancedOptions.noconversion')
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15 $advancedOptions.noconversion
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16 $advancedOptions.verbose
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17 $advancedOptions.gquad
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18 $advancedOptions.circ
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19 $advancedOptions.logml
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20 $advancedOptions.notetra
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21 #end if
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22 ]]>
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23 </command>
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24
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25 <inputs>
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26 <param format="text" name="input" type="data" label="Input file"/>
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27 <param name="temperature" size="6" type="float" value="37.0" label="temperature [°C]" help="-T"/>
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28 <param name="dangling" type="select" label="how to treat dangling end energies" help="-d">
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29 <option value="0">0: ignore dangling ends</option>
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30 <option value="1">1: unpaired bases participate in one dangling end only</option>
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31 <option value="2" selected="True">2: unpaired bases participate in all dangling ends</option>
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32 <option value="3">3: allow coaxial stacking</option>
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33 </param>
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34
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35 <conditional name="advancedOptions">
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36 <param name="advancedSelector" type="select" label="advanced options">
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37 <option value="basic">basic Options</option>
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38 <option value="advanced">advanced Options</option>
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39 </param>
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40 <when value="advanced">
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41 <param name="noconversion" type="boolean" truevalue="--noconv" falsevalue="" checked="false" label="No converstion from T->U" help="--noconv"/>
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42 <param name="verbose" type="boolean" truevalue="--verbose" falsevalue="" checked="false" label="Print out energy of each loop in the structure." help="--verbose"/>
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43 <param name="gquad" type="boolean" truevalue="--gquad" falsevalue="" checked="false" label="G-quadruplex formation prediction" help="--gquad"/>
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44 <param name="circ" type="boolean" truevalue="--circ" falsevalue="" checked="false" label="Assume circular RNA" help="--circ"/>
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45 <param name="logml" type="boolean" truevalue="--logML" falsevalue="" checked="false" label="Logarithmic energy functions for multi-loops" help="--logML"/>
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46 <param name="notetra" type="boolean" truevalue="--noTetra" falsevalue="" checked="false" label="No stabilization for loops, hairpins etc." help="--noTetra"/>
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47 </when>
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48 </conditional>
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49 </inputs>
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50 <outputs>
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51 <data format="txt" name="tabularFile"/>
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52 </outputs>
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53 <tests>
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54 <test>
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55 <param name="input" value="rnaeval_input1.fas"/>
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56 <output name="out_file" file="rnaeval_result1.txt"/>
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57 </test>
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58 </tests>
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59 <help>
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60 <![CDATA[
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61 **RNAeval**
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62 RNAeval evaluates the free energy of an RNA molecule in fixed secondary structure. Sequences and structures are read alternately from stdin. The energy in Kcal/Mol is written to stdout.
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63
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64 -----
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65
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66 **Input format**
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67
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68 RNAeval requires one input file in a format similar to the Fasta format. The secondary strucures should be added after the sequence in dot-bracket notation. Sequence and structure can be interupted by an '&' to calculate the co-folding of two RNA-strands.
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71 ------
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72
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73 **Outputs**
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74
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75 First line: the sequence, second line: the structure with its corresponding energy
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76
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78 ]]>
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79 </help>
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80 <expand macro="requirements" />
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81 </tool>