Mercurial > repos > rnateam > remurna

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/remurna commit 6e51a331dbeab2786d8df5fd379ae3a63eb61d83
author rnateam
date Tue, 13 Dec 2016 12:32:11 -0500
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b1f5d49a6f30 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/remurna commit 6e51a331dbeab2786d8df5fd379ae3a63eb61d83
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1 <tool id="remurna" name="remuRNA" version="1.0.0">
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2 <description>Measurement of Single Nucleotide Polymorphism induced Changes of RNA Conformation</description>
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3 <requirements>
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4 <requirement type="package" version="1.0">remurna</requirement>
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5 </requirements>
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6 <stdio>
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7 <exit_code range="1:" />
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8 </stdio>
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9 <command><![CDATA[
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10 touch input.fa &&
b1f5d49a6f30 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/remurna commit 6e51a331dbeab2786d8df5fd379ae3a63eb61d83
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11 python $__tool_directory__/create_input_file.py '$seq' '$snp' input.fa &&
b1f5d49a6f30 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/remurna commit 6e51a331dbeab2786d8df5fd379ae3a63eb61d83
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12 \$(which remuRNA)
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13 --proc="\${GALAXY_SLOTS}" ## number of CPUs
b1f5d49a6f30 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/remurna commit 6e51a331dbeab2786d8df5fd379ae3a63eb61d83
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14 --window=$window
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15 #if $advanced.advanced_selector =="advanced"
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16 --NA=$advanced.NA
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17 #if $advanced.energy == "abs_sig"
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18 --energy='|sig|'
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19 #else
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20 --energy='sig'
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21 #end if
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22 --tmin=$advanced.tmin
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23 --tinc=$advanced.tinc
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24 --tmax=$advanced.tmax
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25 #if $advanced.suffix
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26 --suffix='$advanced.suffix'
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27 #end if
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28 --log=$advanced.log
b1f5d49a6f30 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/remurna commit 6e51a331dbeab2786d8df5fd379ae3a63eb61d83
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29 #if $advanced.sodium
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30 --sodium=$advanced.sodium
b1f5d49a6f30 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/remurna commit 6e51a331dbeab2786d8df5fd379ae3a63eb61d83
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31 #end if
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32 #if $advanced.magnesium
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33 --magnesium=$advanced.magnesium
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34 #end if
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35 $advanced.polymer
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36 $advanced.zip
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37 $advanced.mutations
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38 $advanced.nodangle
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39 #end if
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40 input.fa
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41 > '$outfile'
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42 ]]></command>
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43 <inputs>
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44 <param argument="--seq" type="data" format="fasta" label="Input Alignment File" />
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45 <param argument="--snp" type="data" format="txt" label="SNP" help="remuRNA accepts only a single tag in each call."/>
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46 <param argument="--window" type="integer" value="200" min="1" label="Windows size" help="Compute average distance over windows of size winsize."/>
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47
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48 <conditional name="advanced">
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49 <param name="advanced_selector" type="select" label="Advanced Options">
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50 <option value="basic">Basic options</option>
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51 <option value="advanced">Advanced options</option>
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52 </param>
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53 <when value="basic"></when>
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54 <when value="advanced">
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55 <param argument="--NA" type="select" label="RNA or DNA">
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56 <option value="RNA" selected="true">RNA sequence</option>
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57 <option value="DNA">DNA sequence</option>
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58 </param>
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59 <param argument="--energy" type="select" label="Energy">
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60 <option value="abs_sig" selected="true">|sig|</option>
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61 <option value="sig">sig</option>
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62 </param>
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63
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64 <param argument="--tmin" type="float" value="37.0" label="Min temperature [°C]" help=""/>
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65 <param argument="--tmax" type="float" value="37.0" label="Max temperature [°C]" help=""/>
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66 <param argument="--tinc" type="float" value="1.0" label="Temperature increment [°C]" help=""/>
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67
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68 <param argument="--suffix" type="text" optional="true" label="Suffix" />
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69
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70
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71 <param argument="--sodium" type="float" optional="true" label="Salt concentration" help=""/>
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72 <param argument="--magnesium" type="float" optional="true" label="Magnesium concentration" help=""/>
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73 <param argument="--mutations" type="boolean" truevalue="--mutations" falsevalue="" checked="false" label="Compute relative entropy for all ppossible point mutations" help=""/>
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74 <param argument="--nodangle" type="boolean" truevalue="" falsevalue="--nodangle" checked="true" label="Include dangling energies" help="default, dangling energies will be added for the bases adjacent to a helix on both sides in any case"/>
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75 <param argument="--polymer" type="boolean" truevalue="--polymer" falsevalue="" checked="false" label="Polymer" help=""/>
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76 <param argument="--zip" type="boolean" truevalue="--zip" falsevalue="" checked="false" label="Zip" help=""/>
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77 <param argument="--log" type="select" label="Log level">
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78 <option value="0">0: OFF</option>
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79 <option value="1" selected="true">1: Errors</option>
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80 <option value="2">2: Warnings</option>
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81 <option value="3">3: Info</option>
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82 <option value="4">4: Debug</option>
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83 <option value="5">5: All</option>
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84 </param>
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85 </when>
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86 </conditional>
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87
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88 </inputs>
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89
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90 <outputs>
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91 <data name="outfile" format="tabular" />
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92 </outputs>
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93 <tests>
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94 <test>
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95 <param name="seq" value="seq.fa"/>
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96 <param name="snp" value="snp.txt"/>
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97 <output name="outfile" file="output.tabular"/>
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98 </test>
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99 </tests>
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100 <help><![CDATA[
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101 **What it does**
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102
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103 Measurement of Single-Nucleotide Polymorphism-induced Changes of RNA Conformation
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104
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105 Single-nucleotide polymorphisms (SNPs) are often linked to critical phenotypes such as diseases or responses to vaccines, medications and environmental factors. However, the specific molecular mechanisms by which a causal SNP acts is usually not obvious. Changes in RNA secondary structure emerge as a possible explanation necessitating the development of methods to measure the impact of single-nucleotide variation on RNA structure. To answer this need, remuRNA commutes the relative entropy between the Boltzmann ensembles of the native and a mutant structure.
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106
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107 **Input**
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108
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109 1. Sequence file: must contain one sequence in Fasta format.
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110
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111 2. SNP file: must contain only one tag
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112
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113
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114 **Output**.
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115
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116 SNP MFE(wt) MFE(mu) dMFE H(wt||mu) GCratio
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117
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118 A23G -15.600 -16.000 0.400 0.877 0.336066
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119 ]]></help>
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120
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121 <citations>
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122 <citation type="doi">10.1093/nar/gks1009</citation>
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123 </citations>
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124 </tool>