annotate metagene_annotator.xml @ 1:17c7ab82bfbc draft default tip

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit f66aa9a65aaf45ac4888ca26f5af661f73b46fdc
author galaxyp
date Mon, 18 Mar 2024 12:34:58 +0000
parents b04960a7abf5
children
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17c7ab82bfbc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit f66aa9a65aaf45ac4888ca26f5af661f73b46fdc
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1 <tool id="metagene_annotator" name="MetaGeneAnnotator" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
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2 <description>gene-finding program for prokaryote and phage (used by sixgill)</description>
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3 <macros>
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4 <token name="@TOOL_VERSION@">1.0</token>
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5 <token name="@VERSION_SUFFIX@">1</token>
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6 </macros>
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7 <xrefs>
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8 <xref type="bio.tools">metageneannotator</xref>
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9 </xrefs>
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10 <requirements>
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11 <requirement type="package" version="@TOOL_VERSION@">metagene_annotator</requirement>
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12 <requirement type="package" version="3.10">python</requirement>
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13 </requirements>
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14 <command detect_errors="exit_code"><![CDATA[
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15 #set $output_list = str($output_formats).split(',')
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16 touch mga_output
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17 #for $input in $inputs:
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18 && mga ${input} $multiple_species >> mga_output
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19 #end for
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20 #if 'tsv' in $output_list or 'bed' in $output_list:
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21 && python '$__tool_directory__/convert_mga.py' mga_output -v
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22 #if 'tsv' in $output_list
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23 --tsv '$mga_tsv'
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24 #end if
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25 #if 'bed' in $output_list
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26 --bed '$mga_bed'
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27 #end if
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28 #end if
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29 ]]></command>
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30 <inputs>
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31 <param name="inputs" type="data" format="fasta" multiple="true" label="prokaryote DNA sequences"/>
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32 <param name="multiple_species" type="boolean" truevalue="-m" falsevalue="-s" checked="true"
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33 label="MetaGenomic - Sequences are from multiple organisms" />
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34 <param name="output_formats" type="select" multiple="true" display="checkboxes" label="output formats">
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35 <option value="txt" selected="true">MetaGeneAnnotator text report</option>
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36 <option value="tsv">MetaGeneAnnotator tabular report with sequence columns</option>
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37 <option value="bed">MetaGeneAnnotator in BED format</option>
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38 </param>
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39 </inputs>
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40 <outputs>
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41 <data name="mga_txt" format="txt" from_work_dir="mga_output" label="${tool.name} on ${on_string} metagenefile">
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42 <filter>'txt' in output_formats</filter>
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43 </data>
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44 <data name="mga_tsv" format="tabular" label="${tool.name} on ${on_string} mga table">
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45 <filter>'tsv' in output_formats</filter>
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46 <actions>
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47 <action name="column_names" type="metadata"
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48 default="seq_ID,seq_model,seq_gc,seq_rbs,gene ID,start pos,end pos,strand,frame,complete/partial,gene score,used model,rbs start,rbs end,rbs score"/>
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49 </actions>
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50 </data>
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51 <data name="mga_bed" format="bed" label="${tool.name} on ${on_string} mga bed">
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52 <filter>'bed' in output_formats</filter>
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53 <actions>
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54 <action name="column_names" type="metadata"
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55 default="chrom,chromStart,chromEnd,name,score,strand,thickStart,thickEnd,itemRgb,blockCount,blockSizes,blockStarts"/>
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56 </actions>
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57 </data>
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58 </outputs>
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59 <tests>
1
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60 <test expect_num_outputs="1">
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61 <param name="inputs" value="metasequences.fasta" ftype="fasta"/>
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62 <param name="multiple_species" value="True"/>
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63 <param name="output_formats" value="txt"/>
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64 <output name="mga_txt">
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65 <assert_contents>
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66 <has_text_matching expression="# 1/1\s# gc = 0.275862, rbs = -1\s# self: -" />
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67 <has_text_matching expression="gene_1\t1812\t1994\t-\t0\t11\t14.10\d+\tb\t2002\t2007\t2.11\d+" />
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68 </assert_contents>
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69 </output>
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70 </test>
1
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71 <test expect_num_outputs="1">
0
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72 <param name="inputs" value="metasequences.fasta" ftype="fasta"/>
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73 <param name="multiple_species" value="False"/>
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74 <param name="output_formats" value="txt"/>
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75 <output name="mga_txt">
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76 <assert_contents>
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77 <has_text_matching expression="# 1/1\s# gc = 0.275862, rbs = 0.428571\s# self: b" />
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78 <has_text_matching expression="gene_1\t1812\t1994\t-\t0\t11\t12.48\d+\tb\t2002\t2007\t0.49\d+" />
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79 </assert_contents>
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80 </output>
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81 </test>
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82 <!-- Try these later
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83 <test>
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84 <param name="inputs" value="metasequences1.fasta,metasequences2.fasta" ftype="fasta"/>
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85 <param name="multiple_species" value="True"/>
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86 <param name="output_formats" value="txt"/>
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87 <output name="mga_txt">
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88 <assert_contents>
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89 <has_text_matching expression="# 1/1.*# 10/1" />
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90 <has_text_matching expression="gene_1\t1812\t1994\t-\t0\t11\t14.10\d+\tb\t2002\t2007\t2.11\d+" />
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91 </assert_contents>
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92 </output>
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93 </test>
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94 <test>
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95 <param name="inputs" value="metasequences.fasta" ftype="fasta"/>
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96 <param name="multiple_species" value="True"/>
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97 <param name="output_formats" value="txt,tsv,bed"/>
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98 <output name="mga_txt">
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99 <assert_contents>
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100 <has_text_matching expression="# 1/1\s# gc = 0.275862, rbs = -1\s# self: -" />
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101 <has_text_matching expression="gene_1\t1812\t1994\t-\t0\t11\t14.10\d+\tb\t2002\t2007\t2.11\d+" />
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102 </assert_contents>
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103 </output>
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104 <output name="mga_tsv">
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105 <assert_contents>
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106 <has_text_matching expression="#seq_id\tseq_model\tseq_gc\tseq_rbs" />
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107 <has_text_matching expression="1/1\t-\t0.27\d+\t-1\tgene_1\t1812\t1994\t-\t0\t11\t14.1035\tb\t2002\t2007\t2.11\d+" />
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
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108 </assert_contents>
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109 </output>
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110 <output name="mga_bed">
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111 <assert_contents>
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112 <has_text_matching expression="1/1\t1811\t1994\t1/1:gene_1\t15\t-\t1811\t1994\t0\t1\t183\t0" />
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113 </assert_contents>
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114 </output>
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115 </test>
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116 -->
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117 </tests>
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118 <help><![CDATA[
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119 **MetaGeneAnnotator (mga)**
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120
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121 A gene-finding program for prokaryote and phage.
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122
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123 The gene annotations can be used by sixgill_ when generating metapeptides from metagenomics shotgun sequencing.
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124
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125 .. image:: Sixgill_MetaGeneAnnotator_Workflow.png
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126 :height: 213
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127 :width: 625
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128
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129 usage:
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130 mga [multi-fasta] <-m/-s>
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131
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132 -m (multiple species sequences are individually treated)
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133 -s (single species sequences are treated as a unit)
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134
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135 **Input:**
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136 *A fasta file of metagenomic sequences*
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137
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138
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139 **Outputs:**
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140
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141 *MetaGeneAnnotator text report*
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142 Output from the MetaGeneAnnotator mga application::
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143
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144 # 1/1
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145 # gc = 0.275862, rbs = -1
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146 # self: -
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147 gene_1 1812 1994 - 0 11 14.1035 b 2002 2007 2.11797
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148 # 2/1
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149 # gc = 0.338877, rbs = -1
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150 # self: -
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151 gene_1 1 414 + 0 01 25.748 b . . .
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152 gene_2 614 790 + 0 11 0.774142 b . . .
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153 gene_3 822 1079 + 0 11 20.6507 b . . .
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154
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155 output format description::
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156
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157 # [sequence name]
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158 # gc = [gc%], rbs = [rbs%]
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159 # self: [(b)acteria/(a)rchaea/(p)hage/unused(-)]
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160 [gene ID] [start pos.] [end pos.] [strand] [frame] [complete/partial] [gene score] [used model] [rbs start] [rbs end] [rbs score]
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161
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162 explanations of output column:
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163 *The value of [frame] (0/1/2) indicates the number of surplus (untranslated) nucleotides at the 5'-end of the predicted ORF.
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164 *The value of [score] indicates the estimated score of predicted gene. All predicted genes are more than 0.
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165 *The value of [complete/partial] indicates that the predicted gene structure is whether complete (contains both of start and stop codons[11]) or partial (lacks start[01] or stop[10] or both of them[00]).
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166 *The value of [model] indicates a selected model ((s)elf/(b)acteria/(a)rchaea/(p)hage) for predicting the gene.
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167
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168
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169 *MetaGeneAnnotator tabular report with sequence columns*
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170 The mga output reformated as a tabular file::
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171
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172 #seq_id seq_model seq_gc seq_rbs gene ID start pos end pos strand frame complete/partial gene score used model rbs start rbs end rbs score
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173 1/1 - 0.275862 -1 gene_1 1812 1994 - 0 11 14.1035 b 2002 2007 2.11797
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174 2/1 - 0.338877 -1 gene_1 1 414 + 0 01 25.748 b . . .
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175 2/1 - 0.338877 -1 gene_2 614 790 + 0 11 0.774142 b . . .
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176 2/1 - 0.338877 -1 gene_3 822 1079 + 0 11 20.6507 b . . .
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177
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178
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179 *MetaGeneAnnotator in BED format*
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180 The mga output reformatted as a BED file which can be used to extract the DNA sequences for each gene from the fasta file::
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181
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182 1/1 1811 1994 1/1:gene_1 15 - 1811 1994 0 1 183 0
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183 2/1 0 414 2/1:gene_1 26 + 0 414 0 1 414 0
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184 2/1 613 790 2/1:gene_2 1 + 613 790 0 1 177 0
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185 2/1 821 1079 2/1:gene_3 21 + 821 1079 0 1 258 0
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186
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187
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188 .. _sixgill: https://github.com/dhmay/sixgill
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189 ]]></help>
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190 <citations>
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191 <citation type="doi">10.1093/dnares/dsn027</citation>
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192 </citations>
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193 </tool>