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annotate rnacode.xml @ 0:4bbca35a866a draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit 1973f3035c10db80883d80847ea254289f5cce2a-dirty
author bgruening
date Thu, 17 Sep 2015 16:48:24 -0400
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1 <tool id="rbc_rnacode" name="RNAcode" version="0.3.0">
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2 <description>Analyze the protein coding potential in MSA</description>
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3 <requirements>
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4 <requirement type="package" version="0.3">rnacode</requirement>
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5 </requirements>
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6 <stdio>
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7 <exit_code range="1:" level="fatal" description="Error occurred. Please check Tool Standard Error"/>
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8 <exit_code range=":-1" level="fatal" description="Error occurred. Please check Tool Standard Error"/>
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9 </stdio>
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10 <version_command>RNAcode --version</version_command>
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11 <command>
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12 <![CDATA[
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13 RNAcode
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15 $outputFormat
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16
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17 #if $cutoff and $cutoff is not None
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18 --cutoff $cutoff
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19 #end if
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20
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21 #if $num_samples and $num_samples is not None
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22 --num-samples $num_samples
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23 #end if
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24
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25 $stop_early
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26 $best_region
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27 $best_only
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28
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29 #if $cond_generateEPS.generateEPS == 'create'
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30 --eps
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31 #if $cond_generateEPS.eps_cutoff and $cond_generateEPS.eps_cutoff is not None
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32 --eps-cutoff $cond_generateEPS.eps_cutoff
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33 #end if
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34 #end if
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35
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36 #if $cond_scoringParameters.scoringParameters == 'custom'
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37 --pars "$pars"
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38 #end if
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39
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40 $alignment
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41
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42 #if $outputFormat.value == '--tabular'
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43 --outfile $outFileDefault
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44 #elif $outputFormat.value == '--gtf'
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45 --outfile $outFileGTF
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46 #end if
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47
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48 ]]>
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49 </command>
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50 <inputs>
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51 <param name="alignment" type="data" format="clustal,maf" label="Multiple Alignment" help="Alignment needs to be formatted in ClustalW or MAF format"/>
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52 <param argument="--cutoff" name="cutoff" type="float" optional="true" value="1.0" label="Cutoff" help="Show only regions that have a p-value below the given number. By default all hits are shown."/>
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53 <param argument="--num_samples" name="num_samples" type="integer" optional="true" value="100" label="Number of samples" help="Number of random alignments that are sampled to calculate the p-value. RNAcode estimates the significance of a coding prediction by sampling a given number of random alignments. Default is 100 which gives reasonably stable p-values that are useful for assessing the relevance of a prediction."/>
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54 <param argument="--stop_early" name="stop_early" type="boolean" truevalue="--stop-early" falsevalue="" checked="false" label="Stop early" help="Setting this option stops the sampling process as soon as it is clear that the best hit will not fall below the given p-value cutoff. For example, assume a p-value cutoff of 0.05 (see --cutoff) and a sample size of 1000 is given (see --num-samples). As soon as 50 random samples score better than the original alignment, the process is stopped and all hits in the original alignment are reported as p>0.05 (or by convention as 1.0 in gtf and tabular output)."/>
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55 <param argument="--best_region" name="best_region" type="boolean" truevalue="--best-region" falsevalue="" checked="false" label="Show only best non-overlapping hits" help="By default all positive scoring segments are shown in the output if they fall below the given p-value cutoff. If two hits overlap (different frame or different strand) and --best_region is given only the hit with the highest score is shown. Strong coding regions often lead to statistically significant signals also in other frames. These hits are suppressed by this option and only the correct reading frame is reported."/>
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56 <param argument="--best_only" name="best_only" type="boolean" truevalue="--best-only" falsevalue="" checked="false" label="Show only best hit" help="This options shows only the one single best hit for each alignment."/>
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57 <conditional name="cond_scoringParameters">
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58 <param name="scoringParameters" type="select" label="Scoring parameters" help="">
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59 <option value="default" selected="true">Default</option>
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60 <option value="custom">Custom</option>
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61 </param>
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62 <when value="default"/>
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63 <when value="custom">
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64 <param argument="--pars" name="pars" type="text" label="Scoring parameters as comma separated string:'DELTA,OMEGA,omega,stop_penalty'" help="See the appendix of the Paper for an explanation for the meaning of these parameters. Default: '-10.0,-4.0,-2.0,-8.0'"/>
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65 </when>
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66 </conditional>
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67 <conditional name="cond_generateEPS">
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68 <param name="generateEPS" type="select" label="Create colored plots in EPS format" help="The generated plots are resolution independent vector graphics that can be included in any graphics software. For each high scoring segment below a given cutoff (see --eps-cutoff) a file named hss-N.eps is created (N is the running number of the high scoring segment)">
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69 <option value="create" selected="true">Create Plots</option>
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70 <option value="nocreate">Do not generate EPS plots</option>
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71 </param>
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72 <when value="create">
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73 <param argument="--eps_cutoff" name="eps_cutoff" type="float" optional="true" value="0.05" label="Create plots only for high scoring segments with p better than:" help=""/>
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74 </when>
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75 <when value="nocreate"/>
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76 </conditional>
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77
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78 <param name="outputFormat" type="select" label="Output format">
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79 <option value="--tabular" selected="true">Default</option>
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80 <option value="--gtf">GTF genome annotation file</option>
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81 </param>
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82 </inputs>
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83 <outputs>
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84 <data argument="--outfile" name="outFileDefault" format="tabular" label="${tool.name} on ${on_string}">
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85 <filter>outputFormat == '--tabular'</filter>
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86 </data>
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87 <data argument="--outfile" name="outFileGTF" format="gtf" label="${tool.name} on ${on_string}">
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88 <filter>outputFormat == '--gtf'</filter>
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89 </data>
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90 <collection name="output_eps" type="list" label="Plots for ${tool.name} on ${on_string}">
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91 <filter>cond_generateEPS['generateEPS'] == "create"</filter>
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92 <discover_datasets pattern="(?P&lt;designation&gt;.*)\.eps" directory="eps" ext="eps" visible="false"/>
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93 </collection>
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94 </outputs>
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95 <tests>
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96 <test>
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97 <param name="alignment" value="coding.aln"/>
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98 <param name="generateEPS" value="nocreate"/>
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99 <param name="outputFormat" value="--tabular"/>
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100 <output name="outFileDefault" ftype="tabular" file="rnacode_result1.tabular" compare="sim_size"/>
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101 <!-- sim_size is needed due to rnacode using random sampling: result files differ, better tests should be implemented -->
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102 </test>
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103 <test>
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104 <param name="alignment" value="coding.maf"/>
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105 <param name="generateEPS" value="nocreate"/>
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106 <param name="outputFormat" value="--gtf"/>
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107 <output name="outFileGTF" ftype="gtf" file="rnacode_result2.gtf" compare="sim_size"/>
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108 <!-- sim_size is needed due to rnacode using random sampling: result files differ, better tests should be implemented -->
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109 </test>
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110 </tests>
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111 <help>
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112 <![CDATA[
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113 **RNAcode**
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114 Predicts protein coding regions in an alignment of homologous
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115 nucleotide sequences. The prediction is based on evolutionary
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116 signatures typical for protein genese, i.e. the presence of
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117 synonyomous/conservative nucleotide mutations, conservation of the
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118 reading frame and absence of stop codons.
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119
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120 RNAcode does not rely on any species specific sequence characteristics
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121 whatsoever and does not use any machine learning techniques. The only
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122 input required for RNAcode is a multiple sequence alignment either in
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123 MAF or Clustal W format. RNAcode reports local regions of unusual high
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124 coding potential together with an associated p-value.
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125
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126 **Input alignment**
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127
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128 The input alignment needs to be formatted in ClustalW format or MAF
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129 format (http://genome.ucsc.edu/FAQ/FAQformat#format5). The latter
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130 format allows to include genomic coordinates which can be used to
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131 produce annotation files.
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132
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133 Important: RNAcode uses the first sequence as reference sequence,
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134 i.e. all results and reported coding regions apply to this reference
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135 sequence.
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136
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137 Currently the alignments has to contain at least 3 sequences. Gaps
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138 have to be given as dash ('-'). Unspecified letters given as 'N' are
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139 allowed and treated neutrally during all calculations. No difference is
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140 made between uppercase or lowercase input, i.e. 'softly'-repeat masked
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141 sequences which use lowercase letters for masked regions are treated
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142 the same way as unmasked sequences.
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143
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144 **Output format**
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145
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146 In the default output each prediction is reported on one line by 10 fields.
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147
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148 1. HSS id
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149 Unique running number for each high scoring segment
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150 predicted in one RNAcode call
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151
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152 2. Frame
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153 The reading frame phasing relative to the starting
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154 nucleotide position in the reference sequence. +1 means
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155 that the first nucleotide in the reference sequence is in
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156 the same frame as the predicted coding region. Negative
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157 frames indicate that the predicted regions are on the
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158 reverse complement strand.
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159
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160 3. Length
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161 The length of the predicted region in amino acids
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162
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163 4. From 5. To
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164 The position of the first/last amino acid in the translated
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165 nucleotide sequence of the reference sequence starting
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166 with 1.
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167
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168 6. Name
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169 The name of the reference sequence as given in the input alignment.
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170
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171 7. Start 8. End
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172 The nucleotide position in the reference sequence of the
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173 predicted coding region. If no genomic coordinates are given
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174 (if you provide a CLUSTAL W as input) the first nucleotide position in
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175 the references sequence is set to 1, otherwise the positions are the
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176 1-based genomic coordinates as given in the input MAF file.
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177
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178 9. Score
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179 The coding potential score. High scores indicate high coding potential.
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180
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181 10. P
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182 The p-value associated with the score. This is the probability
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183 that a random alignment with same properties contains an equally good
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184 or better hit.
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185 ]]>
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186 </help>
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187 <citations>
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188 <citation type="doi">10.1261/rna.2536111</citation>
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189 </citations>
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190 </tool>