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annotate tRNAscan.xml @ 2:358f58401cd6 draft default tip

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author bgruening
date Wed, 26 Jul 2017 10:14:05 -0400
parents d788d1abe238
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1 <tool id="trnascan" name="tRNA prediction" version="0.4">
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2 <description>(tRNAscan)</description>
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3 <requirements>
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4 <requirement type="package" version="1.3.1">trnascan-se</requirement>
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5 <requirement type="package" version="1.0.2">infernal</requirement>
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6 <requirement type="package" version="1.70">biopython</requirement>
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7 <requirement type="package" version="2.7">python</requirement>
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8 </requirements>
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9 <command>
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10 <![CDATA[
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11 python '$__tool_directory__/tRNAscan.py'
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12 #if $organism
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13 $organism
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14 #end if
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15 #if $mode
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16 $mode
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17 #end if
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18 #if $showPrimSecondOpt
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19 $showPrimSecondOpt
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20 #end if
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21 #if $disablePseudo
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22 $disablePseudo
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23 #end if
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24 #if $showCodons
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25 $showCodons
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26 #end if
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27 -o
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28 '$tabular_output'
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29 '$inputfile'
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30 '$fasta_output'
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31 ]]>
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32 </command>
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33 <inputs>
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34 <param name="inputfile" type="data" format="fasta" label="Genome Sequence" help="Dataset missing? See TIP below"/>
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35 <param name="organism" type="select" label="Select Organism">
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36 <option value="" selected="true">Eukaryotic</option>
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37 <option value="-G">general tRNA model</option>
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38 <option value="-B">Bacterial</option>
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39 <option value="-A">Archaeal</option>
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40 <option value="-O">Mitochondrial/Chloroplast</option>
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41 </param>
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42 <param name="mode" type="select" label="Select Mode">
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43 <option value="" selected="true">Default</option>
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44 <option value="-C">Covariance model analysis only (slow)</option>
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45 <option value="-T">tRNAscan only</option>
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46 <option value="-E">EufindtRNA only</option>
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47 <option value="--infernal">Infernal cm analysis (max sensitivity, very slow)</option>
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48 <option value="--newscan">Infernal and new cm models</option>
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49 </param>
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50 <param name="disablePseudo" type="boolean" label="Disable pseudogene checking" truevalue="-D" falsevalue="" />
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51 <param name="showPrimSecondOpt" type="boolean" label="Show primary and secondary structure components to Cove scores" truevalue="-H" falsevalue="" />
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52 <param name="showCodons" type="boolean" label="Show codons instead of tRNA anticodons" truevalue="-N" falsevalue="" />
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53 </inputs>
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54 <outputs>
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55 <data format="tabular" name="tabular_output" label="${tool.name} on ${on_string}: tabular" />
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56 <data format="fasta" name="fasta_output" label="${tool.name} on ${on_string}: fasta" />
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57 </outputs>
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58 <tests>
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59 <test>
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60 <param name="inputfile" value="trna_arabidopsis.fasta" ftype="fasta" />
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61 <param name="organism" value="" />
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62 <param name="mode" value="--infernal" /> <!-- Infernal test not working due to cmsearch error-->
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63 <param name="disablePseudo" value="" />
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64 <param name="showPrimSecondOpt" value="" />
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65 <param name="showCodons" value="" />
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66 <output name="fasta_output" file="tRNAscan_eukaryotic_infernal.fasta" ftype="fasta" />
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67 <output name="tabular_output" file="tRNAscan_eukaryotic_infernal.tabular" ftype="tabular" />
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68 </test>
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69 </tests>
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70 <help>
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71 <![CDATA[
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72
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73
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74 **What it does**
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75
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76 tRNAscan-SE_ was designed to make rapid, sensitive searches of genomic
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77 sequence feasible using the selectivity of the Cove analysis package.
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78 We have optimized search sensitivity with eukaryote cytoplasmic and
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79 eubacterial sequences, but it may be applied more broadly with a
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80 slight reduction in sensitivity.
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81
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82 .. _tRNAscan-SE: http://lowelab.ucsc.edu/tRNAscan-SE/
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83
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84 **Input**
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85
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86 Nucleotide sequence in FASTA format.
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87
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88
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89 **Organism**
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90
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91 - search for eukaryotic cytoplasmic tRNAs:
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92
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93 This is the default.
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94
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95 - use general tRNA model:
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96
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97 This option selects the general tRNA covariance model that was trained
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98 on tRNAs from all three phylogenetic domains (Archaea, Bacteria, and
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99 Eukarya). This mode can be used when analyzing a mixed collection of
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100 sequences from more than one phylogenetic domain, with only slight
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101 loss of sensitivity and selectivity. The original publication
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102 describing this program and tRNAscan-SE version 1.0 used this general
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103 tRNA model exclusively. If you wish to compare scores to those found
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104 in the paper or scans using v1.0, use this option. Use of this option
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105 is compatible with all other search mode options described in this
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106 section.
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107
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108 - search for bacterial tRNAs
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109
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110 This option selects the bacterial covariance model for tRNA analysis,
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111 and loosens the search parameters for EufindtRNA to improve detection
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112 of bacterial tRNAs. Use of this mode with bacterial sequences
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113 will also improve bounds prediction of the 3' end (the terminal CAA
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114 triplet).
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115
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116 - search for archaeal tRNAs
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117
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118 This option selects an archaeal-specific covariance model for tRNA
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119 analysis, as well as slightly loosening the EufindtRNA search
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120 cutoffs.
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121
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122 - search for organellar (mitochondrial/chloroplast) tRNAs
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123
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124 This parameter bypasses the fast first-pass scanners that are poor at
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125 detecting organellar tRNAs and runs Cove analysis only. Since true
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126 organellar tRNAs have been found to have Cove scores between 15 and 20
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127 bits, the search cutoff is lowered from 20 to 15 bits. Also,
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128 pseudogene checking is disabled since it is only applicable to
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129 eukaryotic cytoplasmic tRNA pseudogenes. Since Cove-only mode is
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130 used, searches will be very slow (see -C option below) relative to the
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131 default mode.
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132
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133
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134
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135 **Mode**
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136
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137 - search using Cove analysis only (max sensitivity, slow)
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138
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139 Directs tRNAscan-SE to analyze sequences using Cove analysis only.
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140 This option allows a slightly more sensitive search than the default
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141 tRNAscan + EufindtRNA -> Cove mode, but is much slower (by approx. 250
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142 to 3,000 fold). Output format and other program defaults are
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143 otherwise identical to the normal analysis.
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144
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145 - search using Eukaryotic tRNA finder (EufindtRNA) only:
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146
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147 This option runs EufindtRNA alone to search for tRNAs. Since Cove is
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148 not being used as a secondary filter to remove false positives, this
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149 run mode defaults to "Normal" parameters which more closely
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150 approximates the sensitivity and selectivity of the original algorithm
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151 describe by Pavesi and colleagues.
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152
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153 - search using tRNAscan only (defaults to strict search parameters)
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154
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155 Directs tRNAscan-SE to use only tRNAscan to analyze sequences. This
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156 mode will cause tRNAscan to default to using "strict" parameters
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157 (similar to tRNAscan version 1.3 operation). This mode of operation
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158 is faster (about 3-5 times faster than default mode analysis), but
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159 will result in approximately 0.2 to 0.6 false positive tRNAs per Mbp,
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160 decreased sensitivity, and less reliable prediction of anticodons,
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161 tRNA isotype, and introns.
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162
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163 - search using Infernal cm analysis only (max sensitivity, very slow)
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164
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165
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166 - search using Infernal and new cm models instead of Cove
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167
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168
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169
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170 **disable pseudogene checking**
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171
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172 Manually disable checking tRNAs for poor primary or secondary
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173 structure scores often indicative of eukaryotic pseudogenes. This
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174 will slightly speed the program and may be necessary for non-eukaryotic
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175 sequences that are flagged as possible pseudogenes but are known to be
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176 functional tRNAs.
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177
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178
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179 **Show both primary and secondary structure score components to covariance model bit scores**
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180
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181 This option displays the breakdown of the two components of the
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182 covariance model bit score. Since tRNA pseudogenes often have one
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183 very low component (good secondary structure but poor primary sequence
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184 similarity to the tRNA model, or vice versa), this information may be
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185 useful in deciding whether a low-scoring tRNA is likely to be a
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186 pseudogene. The heuristic pseudogene detection filter uses this
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187 information to flag possible pseudogenes -- use this option to see why
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188 a hit is marked as a possible pseudogene. The user may wish to
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189 examine score breakdowns from known tRNAs in the organism of interest
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190 to get a frame of reference.
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191
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192
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193
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194 **Show codons instead of tRNA anticodons**
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195
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196 This option causes tRNAscan-SE to output a tRNA's corresponding codon
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197 in place of its anticodon.
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198
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199
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200
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201 **Example**
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202
2
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203 **input**
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204
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205 >CELF22B7 C.aenorhabditis elegans (Bristol N2) cosmid F22B7
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206 GATCCTTGTAGATTTTGAATTTGAAGTTTTTTCTCATTCCAAAACTCTGT
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207 GATCTGAAATAAAATGTCTCAAAAAAATAGAAGAAAACATTGCTTTATAT
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208 TTATCAGTTATGGTTTTCAAAATTTTCTGACATACCGTTTTGCTTCTTTT
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209 TTTCTCATCTTCTTCAAATATCAATTGTGATAATCTGACTCCTAACAATC
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210 GAATTTCTTTTCCTTTTTCTTTTTCCAACAACTCCAGTGAGAACTTTTGA
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211 ATATCTTCAAGTGACTTCACCACATCAGAAGGTGTCAACGATCTTGTGAG
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212 AACATCGAATGAAGATAATTTTAATTTTAGAGTTACAGTTTTTCCTCCGA
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213 .....
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214
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215
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216 **output**
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217
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218
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219 ======== ====== ===== ====== ==== ========== ====== ====== ========== ==========
1
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220 tRNA Bounds Intron Bonds
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221 -------- ------ ---------------- ---- ---------- ---------------- ---------- ----------
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222 Name # tRNA Begin End tRNA Anti Codon Begin End Cove Score Hit Origin
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223 ======== ====== ===== ====== ==== ========== ====== ====== ========== ==========
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224 CELF22B7 1 12619 12738 Leu CAA 12657 12692 55.12 Bo
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225 CELF22B7 2 19480 19561 Ser AGA 0 0 66.90 Bo
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226 CELF22B7 3 26367 26439 Phe GAA 0 0 73.88 Bo
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227 CELF22B7 4 26992 26920 Phe GAA 0 0 73.88 Bo
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228 CELF22B7 5 23765 23694 Pro CGG 0 0 60.58 Bo
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229 ======== ====== ===== ====== ==== ========== ====== ====== ========== ==========
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230
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231
1
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232 ]]>
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233 </help>
2
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234 <citations>
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235 <citation type="doi">10.1093/nar/25.5.0955</citation>
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44
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236 </citations>
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237 </tool>