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1 <tool id="cofold" name="Cofold" version="0.0.1">
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2 <description>An RNA secondary structure prediction method that takes co-transcriptional folding into account</description>
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3 <requirements>
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4 <requirement type="package" version="0.0.1"></requirement>
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5 </requirements>
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6 <version_command>CoFold --version</version_command>
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7 <stdio>
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8 <exit_code range="1:" />
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9 <exit_code range=":-1" />
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10 <regex match="Error:" />
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11 <regex match="Exception:" />
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12 </stdio>
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13 <command interpreter="python">
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14 <![CDATA[
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15 cofold.py
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16 -i $infile
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17 -o1 $tabularFile
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18 --parameters " -T$temperature -d$dangling
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19 -P $energy_parameter
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20 --distAlpha $distAlpha
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21 --distTau $distTau
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22 #if $advancedOptions.advancedSelector == 'yes':
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23 $advancedOptions.constraint
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24 $advancedOptions.noconversion
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25 $advancedOptions.nolp
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26 $advancedOptions.nogu
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27 $advancedOptions.noclosinggu
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28 $advancedOptions.notetra
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29 $advancedOptions.circular
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30 #end if
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31 ";
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32 count=`ls -l *.ps | wc -l`;
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33 echo '#RNA structures: '\$count > $report;
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34 ]]>
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35 </command>
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36 <inputs>
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37 <param format="fasta" name="infile" type="data" label="FASTA file"/>
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38 <param name="distAlpha" type="float" value="0.5" label="temperature [°C]" help="(--distAlpha)"/>
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39 <param name="distTau" type="float" value="640.0" label="temperature [°C]" help="(--distTau)"/>
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40 <param name="temperature" size="6" type="float" value="37.0" label="temperature [°C]" help="(-T)"/>
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41 <param name="energy_parameter" type="select" label="Thermodynamic energy parameters" help="(-P)">
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42 <option value="rna_turner1999.par" selected="True">Turner 1999</option>
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43 <option value="rna_turner2004.par">Turner 2004</option>
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44 <option value="rna_andronescu2007.par">Andronescu 2007</option>
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45 </param>
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46 <param name="dangling" type="select" label="how to treat dangling end energies" help="(-d)">
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47 <option value="0">0: ignore dangling ends</option>
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48 <option value="1">1: unpaired bases participate in one dangling end only</option>
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49 <option value="2" selected="True">2: unpaired bases participate in all dangling ends</option>
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50 <option value="3">3: allow coaxial stacking</option>
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51 </param>
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52 <conditional name="advancedOptions">
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53 <param name="advancedSelector" type="select" label="Advanced Options">
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54 <option value="no">no</option>
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55 <option value="yes">yes</option>
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56 </param>
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57 <when value="yes">
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58 <param name="constraint" type="boolean" truevalue="--constraint" falsevalue="" checked="false"
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59 label="Calculate structures subject to constraints" help="(--constraint)"/>
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60 <param name="noconversion" type="boolean" truevalue="--noconv" falsevalue="" checked="false"
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61 label="No conversion" help="Do not convert thymine to uracile (T -> U). (--noconv)"/>
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62 <param name="nolp" type="boolean" truevalue="--noLP" falsevalue="" checked="false"
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63 label="No lonely pairs" help="--noLP don't allow lonely pairs. (--noLP)"/>
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64 <param name="nogu" type="boolean" truevalue="--noGU" falsevalue="" checked="false"
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65 label="No GU pairing" help="Don't allow pairing of G and U. (--noGU)"/>
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66 <param name="noclosinggu" type="boolean" truevalue="--noClosingGU" falsevalue="" checked="false"
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67 label="No GU pairing at the ends" help="Don't allow pairing of G and U at the ends of helices. (--noClosingGU)"/>
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68 <param name="notetra" type="boolean" truevalue="--noTetra" falsevalue="" checked="false"
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69 label="No stabilization for loops, hairpins etc." help="(--noTetra)"/>
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70 <param name="circular" type="boolean" truevalue="--circ" falsevalue="" checked="false"
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71 label="Assume circular RNA structure" help="(--circ)"/>
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72 <param name="noPS" type="boolean" truevalue="--noPS" falsevalue="" checked="false"
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73 label="Don't generate PS files" help="(--noPS)"/>
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74 </when>
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75 <when value="no" />
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76 </conditional>
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77 </inputs>
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78 <outputs>
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79 <data name="tabularFile" format="tabular" label="Tabular File"/>
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80 <data name="report" format="txt" label="RNA PS File" hidden="true">
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81 <discover_datasets pattern="(?P<designation>.+)\.ps" ext="rna_eps" visible="true"/>
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82 </data>
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83 </outputs>
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84 <tests>
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85 <test>
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86 <param name="infile" value="cofold1.fasta" ftype="fasta"/>
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87 <param name="noPS" value="--noPS"/>
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88 <output name="tabularFile" file="colfold_results1.tabular" ftype="tabular" />
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89 </test>
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90 <test>
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91 <param name="infile" value="cofold1.fasta" ftype="fasta"/>
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92 <param name="noPS" value="--noPS"/>
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93 <param name="energy_parameter" value="rna_andronescu2007.par"/>
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94 <param name="dangling" value="1"/>
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95 <param name="advancedSelector" value="yes"/>
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96 <output name="tabularFile" file="colfold_results2.tabular" ftype="tabular" />
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97 </test>
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98 <test>
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99 <param name="infile" value="cofold1.fasta" ftype="fasta"/>
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100 <param name="noPS" value=""/>
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101 <output name="tabularFile" file="colfold_results3.tabular" ftype="tabular" />
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102 <output name="report">
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103 <assert_contents>
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104 <has_line_matching expression="#RNA structures.*" />
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105 </assert_contents>
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106 <discovered_dataset designation="example1_ss" file="example1_ss.ps" compare="sim_size" delta="100" ftype="rna_eps"/>
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107 </output>
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108 </test>
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109 </tests>
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110 <help>
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111 <![CDATA[
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112 **CoFold**
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113
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114 A tool for prediction of RNA secondary structure that takes co-transcriptional folding into account
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115
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116 **Input format**
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117
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118 CoFold requires one input file in FASTA format.
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119
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120 ------
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121
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122 **Outputs**
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123
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124 - Tab-seperated file
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125 - 1st column: header line of FASTA input
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126 - 2nd column: sequence
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127 - 3rd column: dot-bracket notation
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128 - 4th column: free energy
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129
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130 ]]>
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131 </help>
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132 <citations>
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133 <citation type="doi">doi:10.1093/nar/gkt174</citation>
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134 <citation type="doi">doi:10.1093/nar/gks241</citation>
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135 </citations>
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136 </tool>
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