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annotate braker3.xml @ 10:0be6820e3268 draft default tip

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planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit 43caacb959b2d7b842e71737bd645be7ad155a04
author genouest
date Thu, 17 Jul 2025 10:35:48 +0000
parents bec8f57c9d8e
children
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3c0865d1172f planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit d6e73c0417506d93c905b4aeb77d92350b662fbb
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1 <tool id="braker3" name="BRAKER3" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05">
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2 <description>genome annotation</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
7
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6 <xrefs>
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7 <xref type="bio.tools">braker3</xref>
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8 </xrefs>
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9 <requirements>
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10 <expand macro="requirements"/>
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11 </requirements>
9
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12 <command detect_errors="exit_code"><![CDATA[
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0be6820e3268 planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit 43caacb959b2d7b842e71737bd645be7ad155a04
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14 ## Copy Augustus config dir to work dir, to make sure it's writable when running with containers
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15 cp -r "\$AUGUSTUS_CONFIG_PATH/" augustus_dir/ &&
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16 export AUGUSTUS_CONFIG_PATH=`pwd`/augustus_dir/ &&
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0be6820e3268 planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit 43caacb959b2d7b842e71737bd645be7ad155a04
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18
0
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19 braker.pl
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20 --genome '${genome}'
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21 $softmasking
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3c0865d1172f planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit d6e73c0417506d93c905b4aeb77d92350b662fbb
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23 #if $evidences.bam:
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24 --bam ${evidences.bam}
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25 #end if
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3c0865d1172f planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit d6e73c0417506d93c905b4aeb77d92350b662fbb
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27 #if $evidences.prot_seq:
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28 --prot_seq ${evidences.prot_seq}
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29 #end if
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30
3c0865d1172f planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit d6e73c0417506d93c905b4aeb77d92350b662fbb
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31 ## No hints, use esmode
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32 #if not $evidences.bam and not $evidences.prot_seq
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33 --esmode
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34 #end if
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36 #if $output_format == 'gff3'
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37 --gff3
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38 #end if
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39
3c0865d1172f planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit d6e73c0417506d93c905b4aeb77d92350b662fbb
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40 $genemark.fungus
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3c0865d1172f planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit d6e73c0417506d93c905b4aeb77d92350b662fbb
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42 $augustus.crf
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43 --rounds $augustus.rounds
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44 $augustus.AUGUSTUS_ab_initio
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45 $augustus.keepCrf
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46
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47 ##$advanced.UTR
0
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3c0865d1172f planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit d6e73c0417506d93c905b4aeb77d92350b662fbb
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49 $advanced.filterOutShort
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3c0865d1172f planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit d6e73c0417506d93c905b4aeb77d92350b662fbb
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51 #if $advanced.eval:
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52 --eval ${advanced.eval}
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53 #end if
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54
3c0865d1172f planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit d6e73c0417506d93c905b4aeb77d92350b662fbb
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55 #if $advanced.eval_pseudo:
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56 --eval_pseudo ${advanced.eval_pseudo}
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57 #end if
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58
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59 #if $species:
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60 --species '$species'
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61 #end if
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62
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63 $advanced.alternatives_from_evidence
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64
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65 #if $dev.splice_sites:
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66 --splice_sites '$dev.splice_sites'
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67 #end if
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68
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69 #if $dev.min_contig:
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70 --min_contig $dev.min_contig
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71 #end if
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72
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73 --gc_probability $dev.gc_probability
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74 --downsampling_lambda $dev.downsampling_lambda
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75
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76 #if $dev.gm_max_intergenic:
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77 --gm_max_intergenic $dev.gm_max_intergenic
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78 #end if
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79
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80 --threads \${GALAXY_SLOTS:-2}
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81 --useexisting
0
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82 ]]></command>
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83
0
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84 <inputs>
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85 <param argument="--genome" type="data" format="fasta" label="Assembly to annotate" help="The assembly should preferably be soft-masked (with RepeatMasker for example)" />
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86
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87 <param argument="--softmasking" type="boolean" checked="true" truevalue="" falsevalue="--softmasking_off" label="Genome sequence is soft-masked" />
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88
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89 <param argument="--species" type="text" label="Species name" optional="true" help="Using Sp_1, if no species is assigned"/>
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90
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91 <section name="evidences" expanded="true" title="Evidences">
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92 <param argument="--bam" type="data" format="bam" optional="true" label="RNA-seq mapped to genome to train Augustus/GeneMark" />
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93 <param argument="--prot_seq" type="data" format="fasta" optional="true" label="Proteins to map to genome" />
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94 </section>
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95
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96 <section name="genemark" expanded="true" title="GeneMark">
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97 <param argument="--fungus" type="boolean" checked="false" truevalue="--fungus" falsevalue="" label="Fungal genome" help="GeneMark-EX option, run algorithm with branch point model (most useful for fungal genomes)" />
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98 </section>
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99
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100 <section name="augustus" expanded="true" title="Augustus">
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101 <param argument="--crf" type="boolean" checked="false" truevalue="--crf" falsevalue="" label="Use CRF training for Augustus" help="Alternate training method (Conditional Random Field)" />
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102 <param argument="--rounds" type="integer" value="5" label="Number of optimization rounds used in optimize_augustus.pl" />
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103 <param argument="--AUGUSTUS_ab_initio" type="boolean" checked="false" truevalue="--AUGUSTUS_ab_initio" falsevalue="" label="Output ab initio predictions by AUGUSTUS"/>
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104 <param argument="--keepCrf" type="boolean" checked="false" truevalue="--keepCrf" falsevalue="" label="CRF parameters" help="keep CRF parameters even if they are no better than HMM parameters"/>
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105 </section>
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106
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107 <section name="advanced" expanded="false" title="Advanced">
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108 <!--param argument="-\-UTR" type="boolean" checked="false" truevalue="-\-UTR=on" falsevalue="" label="" help="Experimental, requires RNASeq data (bam) and a softmasked genome" /-->
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109 <param argument="--filterOutShort" type="boolean" checked="false" truevalue="--filterOutShort" falsevalue="" label="Filter out too short training gene predicted by GeneMark-EX" />
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110 <param argument="--eval" type="data" format="gtf" optional="true" label="Reference set to evaluate predictions" help="using evaluation scripts from GaTech" />
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111 <param argument="--eval_pseudo" type="data" format="gff3" optional="true" label="File with pseudogenes that will be excluded from accuracy evaluation" />
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112 <param argument="--alternatives-from-evidence" type="boolean" checked="true" truevalue="--alternatives-from-evidence=true" falsevalue="--alternatives-from-evidence=false" label="Output alternative transcripts based on explicit evidence from hints"/>
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113 </section>
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114
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115 <section name="dev" expanded="false" title="Expert options">
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116 <param argument="--splice_sites" type="text" label="List of splice site patterns for UTR prediction" help="Only affects UTR training example generation, not gene prediction by AUGUSTUS (default: GTAG"/>
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117 <param argument="--min_contig" type="integer" optional="true" label="Minimal contig length for GeneMark-EX"/>
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118 <param argument="--gc_probability" type="float" min="0" max="1" value="0.001" label="Probablity for donor splice site pattern GC for gene prediction with GeneMark-EX"/>
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119 <param argument="--gm_max_intergenic" type="integer" optional="true" label="Maximum allowed size of intergenic regions in GeneMark-EX" help="If not set, the value is automatically determined by GeneMark-EX"/>
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120 <param argument="--downsampling_lambda" type="integer" min="0" value="2" label="Lambda parameter of the Poisson distribution" help="for downsampling of training gene structures according to their number of introns distribution"/>
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121 </section>
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122
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123 <param name="output_format" type="select" label="Output format">
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124 <option value="gtf" selected="true">GTF</option>
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125 <option value="gff3">GFF3</option>
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126 </param>
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127 </inputs>
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128
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129 <outputs>
3
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130 <data name='output_gtf' format='gtf' label="${tool.name} on ${on_string}: GTF Annotation" from_work_dir="braker/braker.gtf">
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131 <filter>output_format == 'gtf'</filter>
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132 </data>
3
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133 <data name='output_gff' format='gff3' label="${tool.name} on ${on_string}: GFF Annotation" from_work_dir="braker/braker.gff3">
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134 <filter>output_format == 'gff3'</filter>
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135 </data>
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136 </outputs>
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137
0
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138 <tests>
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139 <test expect_failure="true">
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140 <param name="genome" value="genome_masked.fa"/>
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141 <section name="evidences">
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142 <param name="bam" value="SRR7458692.bam"/>
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143 </section>
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144 <param name="output_format" value="gtf" />
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145 </test>
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146 </tests>
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147
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148 <!-- <test expect_num_outputs="1">
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149 <param name="genome" value="genome_masked.fa" />
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150 <section name="augustus">
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151 <param name="rounds" value="2" />
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152 </section>
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153 <section name="evidences">
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154 <param name="bam" value="SRR7458692.bam" />
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155 </section>
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156 <param name="output_format" value="gtf" />
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157 <output name="output_gtf" file="out_genome/braker.gtf" sort="true"/>
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158 </test>
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159
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160 <test expect_num_outputs="1">
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161 <param name="genemark_license" value="gm_key_64" />
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162 <param name="genome" value="genome_masked.fa" />
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163 <section name="augustus">
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164 <param name="rounds" value="2" />
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165 </section>
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166 <section name="evidences">
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167 <param name="bam" value="SRR7458692.bam" />
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168 <param name="prot_seq" value="proteins.fa" />
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169 </section>
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170 <param name="output_format" value="gff3" />
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171 <output name="output_gff" file="out_genome/braker.gff3"/>
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172 </test>
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173
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174 <test expect_num_outputs="1">
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175 <param name="genemark_license" value="gm_key_64" />
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176 <param name="genome" value="genome_masked.fa" />
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177 <section name="augustus">
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178 <param name="rounds" value="2" />
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179 </section>
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180 <section name="evidences">
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181 <param name="prot_seq" value="proteins.fa" />
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182 </section>
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183 <param name="output_format" value="gff3" />
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184 <output name="output_gff" file="out_genome/braker.gff3"/>
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185 </test> -->
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186
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187
0
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188 <help><![CDATA[
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189
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190 Braker3_ allows for fully automated training of the gene prediction tools GeneMark-EX and AUGUSTUS from RNA-Seq and/or protein homology information, and that integrates the extrinsic evidence from RNA-Seq and protein homology information into the prediction.
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191
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192 In contrast to other available methods that rely on protein homology information, BRAKER3 reaches high gene prediction accuracy even in the absence of the annotation of very closely related species and in the absence of RNA-Seq data.
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193
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194 .. _Braker3: https://github.com/Gaius-Augustus/BRAKER
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195 ]]></help>
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196 <expand macro="citations" />
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197 </tool>