annotate rnapdist.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="rnapdist" name="RNApdist" version="2.1.6.0">
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2 <description>Calculate distances between thermodynamic RNA secondary structure ensembles
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3 </description>
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4 <expand macro="requirements" />
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5 <expand macro="version_command" />
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6 <expand macro="stdio" />
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7 <macros>
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8 <token name="@EXECUTABLE@">RNApdist</token>
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9 <import>macros.xml</import>
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10 </macros>
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11 <command>
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12 <![CDATA[
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13 RNApdist < $input > $output
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14 --compare=$compare
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15 -T$temperature -d$dangling
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16 $backtrack
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17
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18 #if $varExists('$advancedOptions.nolp')
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19 $advancedOptions.noconv
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20 $advancedOptions.nolp
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21 $advancedOptions.nogu
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22 $advancedOptions.noclosinggu
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23 $advancedOptions.notetra
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24 #end if
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25
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26 #if $backtrack and str($compare)=="m"
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27 ; cat backtrack.file >> $outfile
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28 #end if
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29
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30 ]]>
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31 </command>
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32
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33 <inputs>
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34 <param format="fasta" name="input" type="data" label="Fasta file"/>
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35 <param name="temperature" size="6" type="float" value="37.0" label="temperature [°C]" help="-T"/>
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36 <param name="dangling" type="select" label="how to treat dangling end energies" help="-d">
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37 <option value="0">0: ignore dangling ends</option>
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38 <option value="1">1: unpaired bases participate in one dangling end only</option>
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39 <option value="2" selected="True">2: unpaired bases participate in all dangling ends</option>
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40 <option value="3">3: allow coaxial stacking</option>
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41 </param>
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42 <param name="compare" type="select" label="Comparison Option" help="-d">
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43 <option value="p" selected="True">p: pairwise (1st with 2nd, 3rd with 4th, ...)</option>
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44 <option value="m">m: matrix (each with each, output in matrix form)</option>
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45 <option value="f" >f: first (1st with 2nd, 1st with 3rd, ...)</option>
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46 <option value="c">c: continuous (1st with 2nd, 2nd with 3rd, ...)</option>
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47 </param>
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48 <param name="backtrack" type="boolean" checked="false" truevalue="--backtrack" falsevalue="" label="Print an alignment" help="--backtrack"/>
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49 <conditional name="advancedOptions">
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50 <param name="advancedSelector" type="select" label="advanced options">
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51 <option value="basic">basic Options</option>
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52 <option value="advanced">advanced Options</option>
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53 </param>
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54 <when value="advanced">
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55 <param name="noconv" type="boolean" truevalue="--noconv" falsevalue="" checked="false" label="No conversion of T -> U" help="--noconv"/>
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56 <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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57 <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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58 <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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59 <param name="notetra" type="boolean" truevalue="--noTetra" falsevalue="" checked="false" label="No stabilization for loops, hairpins etc." help="--noTetra"/>
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60 </when>
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61 </conditional>
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62 </inputs>
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63 <outputs>
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64 <data format="txt" name="output"/>
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65 <data format="txt" name="dotplot">
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66 <collection name="matrix_outputs" type="list" label="rna_eps outputs">
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67 <discover_datasets pattern="(?P&lt;designation&gt;.+)_dp\.ps" ext="rna_eps" visible="true"/>
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68 </collection>
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69 </outputs>
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70 <tests>
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71 </tests>
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72 <help>
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73 <![CDATA[
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74
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75 **RNApdist**
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76
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77 RNApdist calculates structure distances between the thermodynamic ensembles of the secondary structures of RNA sequences.
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78
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79 -----
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80
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81 **Input format**
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82
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83 RNApdist requires one input file
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84 - Fasta file
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85
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86 ------
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87
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88 **Outputs**
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89
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90 - output of alignment scores and alignments (if -B option is selected)
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91 - dot plot matrices in postscript format bundled together in a tar file
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92
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93 ]]>
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94 </help>
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95 <expand macro="requirements" />
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96 </tool>