annotate rnaalifold.xml @ 0:78d673470d45 draft

Imported from capsule None
author rnateam
date Wed, 04 Feb 2015 12:05:27 -0500
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children 5e58cbf27a05
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1 <tool id="rnaalifold" name="RNAalifold" version="2.1.6.0">
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2 <description>Calculate minimum free energy secondary structures and partition function on a multiple alignment file</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@">RNAalifold</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 RNAalifold < $input > $tabularFile
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13 -T$temperature -d$dangling
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14 $pf
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15 $mis
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16 #if $measelect.mea=="yes"
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17 --mea=$measelect.meavalue
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18 #end if
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19 #if $backtrackselect.backtrack=="yes"
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20 --stochBT_en=$backtrackselect.backtrackvalue
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21 #end if
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22 #if $varExists('$advancedOptions.color')
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23 $advancedOptions.alignment
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24 $advancedOptions.color
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25 $advancedOptions.gquad
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26 $advancedOptions.nolp
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27 $advancedOptions.nogu
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28 $advancedOptions.noclosinggu
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29 $advancedOptions.notetra
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30 $advancedOptions.canonicalonly
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31 $advancedOptions.circular
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32 --cfactor=$advancedOptions.cfactor
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33 --nfactor=$advancedOptions.nfactor
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34 $advancedOptions.endgaps
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35 $advancedOptions.ribosum
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36 #end if
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37 ; tar -cf $imagesFile *.ps
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38 ]]>
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39 </command>
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40 <inputs>
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41 <param format="clustal" name="input" type="data" label="Clustal file"/>
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42 <param name="temperature" size="6" type="float" value="37.0" label="temperature [°C]" help="-T"/>
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43 <param name="dangling" type="select" label="how to treat dangling end energies" help="-d">
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44 <option value="0">0: ignore dangling ends</option>
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45 <option value="1">1: unpaired bases participate in one dangling end only</option>
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46 <option value="2" selected="True">2: unpaired bases participate in all dangling ends</option>
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47 <option value="3">3: allow coaxial stacking</option>
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48 </param>
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49 <param name="pf" type="boolean" checked="false" truevalue="-p" falsevalue="" label="calculate partition function" help="-p"/>
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50 <param name="mis" type="boolean" checked="false" truevalue="--mis" falsevalue="" label="Most Informative Sequence" help="--mis"/>
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51 <conditional name="measelect">
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52 <param name="mea" type="select" label="calculate maximum expected accuracy" help="--MEA">
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53 <option value="no">no</option>
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54 <option value="yes">yes</option>
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55 </param>
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56 <when value="yes">
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57 <param name="meavalue" size="6" type="float" value="1.0" label="Gamma Value"/>
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58 </when>
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59 </conditional>
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60 <conditional name="backtrackselect">
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61 <param name="backtrack" type="select" label="number of structures" help="--stochBT_en">
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62 <option value="no">no</option>
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63 <option value="yes">yes</option>
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64 </param>
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65 <when value="yes">
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66 <param name="backtrackvalue" size="4" type="integer" value="1" label="Number of random structures."/>
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67 </when>
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68 </conditional>
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69 <conditional name="advancedOptions">
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70 <param name="advancedSelector" type="select" label="advanced options">
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71 <option value="basic">basic Options</option>
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72 <option value="advanced">advanced Options</option>
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73 </param>
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74 <when value="advanced">
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75 <param name="alignment" type="boolean" truevalue="--aln" falsevalue="" checked="false" label="Colored and annotated alignment image" help="--color"/>
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76 <param name="color" type="boolean" truevalue="--color" falsevalue="" checked="false" label="Colored secondary structure image" help="--color"/>
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77 <param name="gquad" type="boolean" truevalue="--gquad" falsevalue="" checked="false" label="G Quadruplex formation" help="-g take into account G Quadruplex formation"/>
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78 <param name="nolp" type="boolean" truevalue="--noLP" falsevalue="" checked="false" label="No lonely pairs" help="--noLP don't allow lonely pairs."/>
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79 <param name="nogu" type="boolean" truevalue="--noGU" falsevalue="" checked="false" label="No GU pairing" help="--noGU don't allow pairing of G and U."/>
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80 <param name="noclosinggu" type="boolean" truevalue="--noClosingGU" falsevalue="" checked="false" label="No GU pairing at the ends" help="--noClosingGU don't allow pairing of G and U at the ends of helices."/>
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81 <param name="notetra" type="boolean" truevalue="--noTetra" falsevalue="" checked="false" label="No stabilization for loops, hairpins etc." help="--noTetra"/>
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82 <param name="canonicalonly" type="boolean" truevalue="--canonicalBPonly" falsevalue="" checked="false" label="Canonical basepairing only" help="--canonicalBPonly"/>
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83 <param name="circular" type="boolean" truevalue="--circ" falsevalue="" checked="false" label="Assume circular RNA structure" help="--circ"/>
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84 <param name="cfactor" size="6" type="float" value="1.0" label="Weight of the covariance term" help="--cfactor"/>
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85 <param name="nfactor" size="6" type="float" value="1.0" label="Penalty for non-compatible sequences in the covariance term" help="--nfactor"/>
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86 <param name="endgaps" type="boolean" truevalue="--endgaps" falsevalue="" checked="false" label="Score pairs with endgaps same as gap-gap pairs" help="--endgaps"/>
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87 <param name="ribosum" type="boolean" truevalue="--ribosum_scoring" falsevalue="" checked="false" label="Use ribosum scoring matrix" help="--ribosum_scoring"/>
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88 </when>
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89 </conditional>
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90 </inputs>
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91 <outputs>
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92 <data format="txt" name="tabularFile"/>
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93 <data format="tar" name="imagesFile"/>
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94 </outputs>
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95 <tests>
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96 </tests>
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97 <help>
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98 <![CDATA[
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99 **RNAalifold**
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100
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101 -----
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102
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103 **Input format**
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104
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105 RNAalifold requires one input file
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106 - Clustal file
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107
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108 ------
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109
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110 **Outputs**
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111
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112 - energy of the consensus structures in the clustal file
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113 - several possible postscript images bundled together in a tar file
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114
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115
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116 ]]>
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117 </help>
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118 <expand macro="requirements" />
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119 </tool>