annotate funannotate_predict.xml @ 2:33092577d65d draft

"planemo upload commit c70e2e82ba7d3f9ee43c101ab267cdf0847d8864"
author iuc
date Thu, 21 Oct 2021 07:32:20 +0000
parents 1a59958c1f76
children 73909ee8162e
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1 <tool id="funannotate_predict" name="Funannotate predict annotation" profile="20.01" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
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2 <description></description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <requirements>
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7 <expand macro="requirements" />
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8 </requirements>
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9 <version_command><![CDATA[funannotate check --show-versions]]></version_command>
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10 <command><![CDATA[
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11 #if $genemark.genemark_license:
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12 if [ -z "\$GENEMARK_PATH" ] ; then echo "GeneMark is not installed on this Galaxy server." >&2 ; exit 1 ; fi &&
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13 if [ ! -f "\$GENEMARK_PATH/gmes_petap.pl" ] ; then echo "GeneMark is not installed properly on this Galaxy server." >&2 ; exit 1 ; fi &&
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14 ## GeneMark only search for license in ~/.gm_key
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15 cp '${genemark.genemark_license}' ~/.gm_key &&
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16 #end if
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17
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18 #if $uglyTestingHack == "true":
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19 ## funannotate_db contains some hard coded path, need to rewrite one for tests (not in real life when using data manager)
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20 ## Need to copy too as the test_data is read only on CI
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21 cp -r '${database.fields.path}' './hacked_database' &&
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22 sed -i.bak 's|/tmp/prout|'`pwd`'/hacked_database|' './hacked_database/trained_species/fly/info.json' &&
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23 #end if
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24
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25 funannotate predict
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26 --input '${input}'
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27 --out output
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28
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29 #if $uglyTestingHack == "true":
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30 --database `pwd`'/hacked_database'
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31 #else
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32 --database '$database.fields.path'
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33 #end if
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34
1
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35 $force
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36
0
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37 --species '${organism.species}'
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38 --isolate '${organism.isolate}'
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39 --strain '${organism.strain}'
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40 --organism '${organism.organism}'
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41 --ploidy ${organism.ploidy}
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42 --SeqCenter '${organism.SeqCenter}'
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43 --SeqAccession '${organism.SeqAccession}'
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44 --name '${organism.name}'
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45 --numbering ${organism.numbering}
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46
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47 #if $parameters:
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48 --parameters '${parameters}'
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49 #end if
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50
1
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51 #if $evidences.rna_bam
0
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52 --rna_bam ${evidences.rna_bam}
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53 #end if
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54
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55 #set est_list = ""
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56 #if len($evidences.transcript_evidence) > 0:
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57 #for $estev in $evidences.transcript_evidence:
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58 #if $estev:
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59 #set est_list += " '" + str($estev) + "'"
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60 #end if
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61 #end for
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62 #end if
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63 #if $est_list:
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64 --transcript_evidence $est_list
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65 #end if
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66
2
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67 #if $evidences.prot_evidence.prot_evidence_source == 'custom':
0
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68 --protein_evidence
2
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69 #for $protev in $evidences.prot_evidence.protein_evidence:
0
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70 '${protev}'
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71 #end for
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72 #end if
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73 --p2g_pident ${evidences.p2g_pident}
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74 --p2g_prefilter ${evidences.p2g_prefilter}
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75
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76 --busco_seed_species '${busco.busco_seed_species}'
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77 --busco_db '${busco.busco_db}'
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78
0
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79 #if $augustus.augustus_species != 'none':
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80 --augustus_species '${augustus.augustus_species}'
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81 #end if
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82 --min_training_models ${augustus.min_training_models}
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83 ${augustus.optimize_augustus}
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84
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85 #if $genemark.genemark_license:
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86 --genemark_mode '${genemark.genemark_mode}'
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87 #if $genemark.genemark_mod:
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88 --genemark_mod '${genemark.genemark_mod}'
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89 #end if
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90 --soft_mask ${genemark.soft_mask}
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91 #end if
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92
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93 $evm.repeats2evm
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94 #if $evm.evm_partitioning.evm_partition == "yes":
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95 --evm-partition-interval ${evm.evm_partitioning.evm_partition_interval}
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96 #else:
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97 --no-evm-partitions
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98 #end if
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99 #if $evm.weights:
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100 --weights '${evm.weights}'
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101 #end if
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102
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103 #if $other_predictors.stringtie:
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104 --stringtie '${other_predictors.stringtie}'
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105 #end if
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106 #if $other_predictors.maker_gff:
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107 --maker_gff '${other_predictors.maker_gff}'
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108 #end if
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109 #if $other_predictors.pasa_gff:
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110 --pasa_gff '${other_predictors.pasa_gff}:${other_predictors.pasa_gff_weight}'
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111 #end if
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112 #if $other_predictors.other_gff:
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113 --other_gff '${other_predictors.other_gff}:${other_predictors.other_gff_weight}'
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114 #end if
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115
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116 --min_intronlen ${filtering.min_intronlen}
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117 --max_intronlen ${filtering.max_intronlen}
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118 --min_protlen ${filtering.min_protlen}
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119 ${filtering.keep_no_stops}
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120 --repeat_filter ${filtering.repeat_filter}
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121
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122 --cpus \${GALAXY_SLOTS:-2}
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123
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124 &&
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125
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126 mv output/predict_results/*.gbk out.gbk &&
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127 mv output/predict_results/*.tbl out.tbl &&
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128 mv output/predict_results/*.gff3 out.gff3 &&
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129 mv output/predict_results/*.proteins.fa out.proteins.fa &&
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130 mv output/predict_results/*.mrna-transcripts.fa out.mrna-transcripts.fa &&
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131 mv output/predict_results/*.cds-transcripts.fa out.cds-transcripts.fa &&
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132 mv output/predict_results/*.discrepency.report.txt out.discrepency.report.txt &&
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133 mv output/predict_results/*.error.summary.txt out.error.summary.txt &&
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134 mv output/predict_results/*.validation.txt out.validation.txt &&
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135 mv output/predict_results/*.stats.json out.stats.json
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136 ]]></command>
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137 <inputs>
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138 <param argument="--input" type="data" format="fasta" label="Assembly to annotate" help="The assembly should be soft-masked (with RepeatMasker for example)" />
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139
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140 <param name="database" label="Funannotate database" type="select">
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141 <options from_data_table="funannotate">
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142 <column name="value" index="0" />
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143 <column name="name" index="1" />
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144 <column name="path" index="3" />
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145 <filter type="sort_by" column="0" />
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146 <filter type="static_value" column="2" value="1.0" />
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147 </options>
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148 </param>
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149
1
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150 <param argument="--force" type="boolean" checked="true" truevalue="" falsevalue="--force" label="Check the genome sequence" help="Disable at your own risk if you want to ignore problems in the genome sequence reported by Funannotate" />
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151
0
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152 <section name="organism" expanded="true" title="Organism">
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153 <param argument="--species" type="text" optional="false" label="Name of the species to annotate" help="e.g. Genus species">
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154 <validator type="empty_field" />
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155 </param>
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156 <param argument="--isolate" type="text" label="Isolate name" help="If relevant (e.g. Af293)" />
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157 <param argument="--strain" type="text" label="Strain name" help="If relevant (e.g. FGSCA4)" />
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158 <param argument="--organism" type="boolean" checked="false" truevalue="fungus" falsevalue="other" label="Is it a fungus species?" />
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159 <param argument="--ploidy" type="integer" value="1" label="Ploidy of assembly" />
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160 <param argument="--SeqCenter" type="text" value="CFMR" label="Sequencing facility for NCBI tbl file" />
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161 <param argument="--SeqAccession" type="text" value="12345" label="Sequence accession number for NCBI tbl file" />
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162 <param argument="--name" type="text" value="FUN_" label="Locus tag prefix" help="Will prefix all the gene names" />
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163 <param argument="--numbering" type="integer" value="1" label="Specify where gene numbering starts" />
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164 </section>
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165
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166 <section name="evidences" expanded="true" title="Evidences">
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167 <param argument="--rna_bam" type="data" format="bam" optional="true" label="RNA-seq mapped to genome to train Augustus/GeneMark-ET" />
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168 <param argument="--transcript_evidence" type="data" format="fasta" multiple="true" optional="true" label="mRNA/ESTs to align to genome" />
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169 <conditional name="prot_evidence">
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170 <param name="prot_evidence_source" type="select" label="Select protein evidences">
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171 <option value="uniprot" selected="True">Use UniProtKb/SwissProt (from selected Funannotate database)</option>
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172 <option value="custom">Custom protein sequences</option>
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173 </param>
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174 <when value="uniprot"/>
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175 <when value="custom">
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176 <param argument="--protein_evidence" type="data" format="fasta" multiple="true" label="Proteins to map to genome" />
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177 </when>
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178 </conditional>
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179 <param argument="--p2g_pident" type="integer" value="80" label="Exonerate percent identity (for proteins)" />
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180 <param argument="--p2g_prefilter" type="select" label="Prefilter hists with (for proteins)">
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181 <option value="diamond" selected="True">Diamond</option>
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182 <option value="tblastn">tblastn (slower)</option>
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183 </param>
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184 </section>
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185
1
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186 <section name="busco" expanded="true" title="Busco">
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187 <param argument="--busco_db" type="select" label="BUSCO models to align" help="BUSCO will be used to perform initial training of ab initio predictors (e.g. Augustus).">
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188 <expand macro="busco_species"/>
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189 </param>
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190 <param argument="--busco_seed_species" type="select" label="Initial Augustus species training set for BUSCO alignment" help="Used when BUSCO runs Augustus internally.">
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191 <expand macro="augustus_species"/>
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192 </param>
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193 </section>
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194
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195 <section name="filtering" expanded="true" title="Filtering">
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196 <param argument="--min_intronlen" type="integer" value="10" label="Minimum intron length" />
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197 <param argument="--max_intronlen" type="integer" value="3000" label="Maximum intron length" />
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198 <param argument="--min_protlen" type="integer" value="50" label="Minimum protein length" />
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199 <param argument="--keep_no_stops" type="boolean" checked="false" truevalue="--keep_no_stops" falsevalue="" label="Keep gene models without valid stops" />
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200 <param argument="--repeat_filter" type="select" label="Repetitive gene model filtering" help="'overlap' drops gene models that are more than 90% contained within a repeat region; 'blast' compares the amino acid sequences to a small database of known transposons">
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201 <option value="overlap blast" selected="True">overlap + blast</option>
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202 <option value="overlap">overlap</option>
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203 <option value="blast">blast</option>
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204 <option value="none">none</option>
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205 </param>
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206 </section>
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207
0
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208 <param argument="--parameters" type="data" format="json" optional="true" label="Ab-initio training parameters from a previous run" help="If specified, will over-rule any other training presets based on sepcies selection." />
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209
1
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210 <section name="augustus" expanded="false" title="Augustus settings (advanced)">
0
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211 <param argument="--augustus_species" type="select" label="Augustus species training set" help="Select a species from the list">
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212 <option value="none" selected="True">No corresponding species, train from scratch</option>
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213 <expand macro="augustus_species"/>
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214 </param>
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215 <param argument="--min_training_models" type="integer" value="200" label="Minimum number of models to train Augustus" />
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216 <param argument="--optimize_augustus" type="boolean" checked="false" truevalue="--optimize_augustus" falsevalue="" label="Run 'optimize_augustus.pl' to refine training (long runtime)" />
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217 </section>
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218
1
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219 <section name="genemark" expanded="false" title="GeneMark settings (advanced)">
0
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220 <param name="genemark_license" type="data" format="txt" optional="true" label="GeneMark license file" help="GeneMark is not a free software, to use it download and unzip a license from http://topaz.gatech.edu/GeneMark/license_download.cgi (ES/ET/EP version). GeneMark needs to be installed manually by Galaxy administrators, it might not be available on this server." />
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221 <param argument="--genemark_mode" type="select" label="GeneMark mode">
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222 <option value="ES" selected="True">ES</option>
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223 <option value="ET">ET</option>
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224 </param>
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225 <param argument="--genemark_mod" type="data" format="txt" optional="true" label="Use pre-existing Genemark training file (e.g. gmhmm.mod)" />
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226 <param argument="--soft_mask" type="integer" value="2000" label="Softmasked length threshold for GeneMark" help="GeneMark will skip prediction on repeat regions shorter than this value" />
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227 </section>
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228
1
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229 <section name="other_predictors" expanded="false" title="Other annotations (advanced)">
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230 <param argument="--stringtie" type="data" format="gtf" optional="true" label="StringTie GTF result" />
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231 <param argument="--maker_gff" type="data" format="gff3" optional="true" label="MAKER2 GFF file" help="Parse results directly to EVM" />
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232 <param argument="--pasa_gff" type="data" format="gff3" optional="true" label="PASA generated gene models" />
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233 <param name="pasa_gff_weight" type="integer" value="1" label="Weight for PASA generated gene models" />
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234 <param argument="--other_gff" type="data" format="gff3" optional="true" label="Annotation pass-through to EVM" />
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235 <param name="other_gff_weight" type="integer" value="1" label="Weight for annotation pass-through to EVM" />
0
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236 </section>
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237
1
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238 <section name="evm" expanded="false" title="EVM settings (advanced)">
0
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239 <param argument="--repeats2evm" type="boolean" checked="false" truevalue="--repeats2evm" falsevalue="" label="Use repeats in EVM consensus model building" help="Not recommended for fungal genomes that have high gene density. You might want to turn this option on for larger genomes or those that have a high repeat content." />
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240 <conditional name="evm_partitioning">
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241 <param name="evm_partition" type="select" label="Split contigs into partitions for EVM processing?" help="Splits big contigs in smaller overlaping chunks to reduce memory usage and parallelize">
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242 <option value="yes" selected="True">Yes</option>
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243 <option value="no">No</option>
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244 </param>
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245 <when value="yes">
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246 <param argument="--evm-partition-interval" type="integer" value="1500" label="Min length between genes to make a partition" />
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247 </when>
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248 <when value="no"/>
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249 </conditional>
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250 <param argument="--weights" type="text" optional="true" label="Custom ab-initio predictor and EVM weight" help="e.g. augustus:2 pasa:10">
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251 <validator type="regex" message="Key must consist of alphanumeric characters only, possibly separated by the period character ('.')">^[\w: ]+$</validator>
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252 </param>
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253 </section>
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254
1
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255 <param name="outputs" type="select" optional="true" multiple="true" label="Which outputs should be generated">
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256 <option value="gbk" selected="true">Annotated genome (genbank)</option>
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257 <option value="tbl">NCBI tbl annotation file (use for NCBI submission)</option>
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258 <option value="gff3">Annotation in GFF3 format</option>
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259 <option value="proteins_fa">Multi-fasta file of protein coding genes</option>
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260 <option value="mrna_transcripts_fa">Multi-fasta file of transcripts (mRNA)</option>
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261 <option value="cds_transcripts_fa">Multi-fasta file of transcripts (CDS)</option>
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262 <option value="tbl2asn_report">tbl2asn summary report of annotated genome</option>
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263 <option value="tbl2asn_error">tbl2asn error summary report</option>
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264 <option value="tbl2asn_validation">tbl2asn genome validation report</option>
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265 <option value="stats">statistics</option>
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266 </param>
0
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267
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268 <!-- Need this to change path in the test funannotate_db -->
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269 <param type="hidden" name="uglyTestingHack" value="" />
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270 </inputs>
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271 <outputs>
1
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272 <data name='annot_gbk' format='genbank' label="${tool.name} on ${on_string}: annotation (genbank)" from_work_dir="out.gbk">
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273 <filter>outputs and 'gbk' in outputs</filter>
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274 </data>
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275 <data name='annot_tbl' format='txt' label="${tool.name} on ${on_string}: NCBI tbl annotation file" from_work_dir="out.tbl">
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276 <filter>outputs and 'tbl' in outputs</filter>
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277 </data>
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278 <data name='annot_gff3' format='gff3' label="${tool.name} on ${on_string}: annotation (GFF3)" from_work_dir="out.gff3">
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279 <filter>outputs and 'gff3' in outputs</filter>
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280 </data>
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281 <data name='fasta_proteins' format='fasta' label="${tool.name} on ${on_string}: protein sequences" from_work_dir="out.proteins.fa">
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282 <filter>outputs and 'proteins_fa' in outputs</filter>
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283 </data>
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284 <data name='fasta_transcripts_mrna' format='fasta' label="${tool.name} on ${on_string}: transcript mRNA sequences" from_work_dir="out.mrna-transcripts.fa">
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285 <filter>outputs and 'mrna_transcripts_fa' in outputs</filter>
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286 </data>
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287 <data name='fasta_transcripts_cds' format='fasta' label="${tool.name} on ${on_string}: transcript CDS sequences" from_work_dir="out.cds-transcripts.fa">
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288 <filter>outputs and 'cds_transcripts_fa' in outputs</filter>
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289 </data>
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290 <data name='tbl2asn_report' format='txt' label="${tool.name} on ${on_string}: tbl2asn summary report of annotated genome" from_work_dir="out.discrepency.report.txt">
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291 <filter>outputs and 'tbl2asn_report' in outputs</filter>
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292 </data>
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293 <data name='tbl2asn_error' format='txt' label="${tool.name} on ${on_string}: tbl2asn error summary report" from_work_dir="out.error.summary.txt">
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294 <filter>outputs and 'tbl2asn_error' in outputs</filter>
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295 </data>
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296 <data name='tbl2asn_validation' format='txt' label="${tool.name} on ${on_string}: tbl2asn genome validation report" from_work_dir="out.validation.txt">
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297 <filter>outputs and 'tbl2asn_validation' in outputs</filter>
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298 </data>
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299 <data name='stats' format='json' label="${tool.name} on ${on_string}: stats" from_work_dir="out.stats.json">
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300 <filter>outputs and 'stats' in outputs</filter>
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301 </data>
0
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302 <!-- TODO some day: provide trained models as output, reusable as input to other funannotate runs
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303 (parameters.json file references files with absolute paths, would probably need to create an archive + edit paths in parameters.json) -->
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304 <!--data name='abinitio' format='json' label="${tool.name} on ${on_string}: ab-initio training parameters" from_work_dir="output/predict_results/*.parameters.json" /-->
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305 </outputs>
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306 <tests>
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307 <!-- training from scratch -->
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308 <test>
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309 <param name="input" value="genome_masked.fa" />
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310 <param name="database" value="2021-07-20-120000" />
1
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311 <section name="busco">
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312 <param name="busco_seed_species" value="fly" />
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313 <param name="busco_db" value="insecta" />
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314 </section>
0
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315 <section name="organism">
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316 <param name="species" value="Genus species" />
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317 </section>
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318 <section name="augustus">
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319 <param name="min_training_models" value="3" />
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320 </section>
1
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321 <param name="outputs" value="gbk,tbl,gff3,proteins_fa,mrna_transcripts_fa,cds_transcripts_fa,tbl2asn_error,tbl2asn_report,tbl2asn_validation,stats" />
0
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322 <!-- non deterministic results, so can't be more precise here -->
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323 <output name="annot_gbk">
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324 <assert_contents>
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325 <has_text text=" TITLE Direct Submission" />
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326 <has_text text="/locus_tag=&quot;FUN_000001&quot;" />
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327 </assert_contents>
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328 </output>
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329 <output name="annot_tbl">
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330 <assert_contents>
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331 <has_text text=">Feature sample" />
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332 <has_text text="gnl|ncbi|FUN_000001-T1_mrna" />
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333 </assert_contents>
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334 </output>
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335 <output name="annot_gff3">
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336 <assert_contents>
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337 <has_text text="##gff-version 3" />
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338 <has_text text="ID=FUN_000001-T1;Parent=FUN_000001;product=hypothetical protein;" />
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339 </assert_contents>
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340 </output>
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341 <output name="fasta_proteins">
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342 <assert_contents>
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343 <has_text text=">FUN_000001-T1 FUN_000001" />
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344 </assert_contents>
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345 </output>
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346 <output name="fasta_transcripts_mrna">
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347 <assert_contents>
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348 <has_text text=">FUN_000001-T1 FUN_000001" />
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
349 </assert_contents>
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
350 </output>
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
351 <output name="fasta_transcripts_cds">
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
352 <assert_contents>
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
353 <has_text text=">FUN_000001-T1 FUN_000001" />
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
354 </assert_contents>
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
355 </output>
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
356 <!--output name="abinitio" file="predict_scratch/fly.parameters.json" compare="sim_size" /-->
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
357 <output name="tbl2asn_report" file="predict_scratch/Genus_species.discrepency.report.txt" compare="sim_size" />
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
358 <output name="tbl2asn_error" file="predict_scratch/Genus_species.error.summary.txt" compare="sim_size" delta="500" />
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
359 <output name="tbl2asn_validation" file="predict_scratch/Genus_species.validation.txt" compare="sim_size" delta="500" />
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
360 <output name="stats" file="predict_scratch/Genus_species.stats.json" compare="sim_size" />
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
361 <assert_stderr>
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
362 <has_text text="augustus busco"/>
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
363 <has_text text="glimmerhmm busco"/>
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
364 <has_text text="snap busco"/>
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
365 <has_text text="Running BUSCO to find conserved gene models for training ab-initio predictors"/>
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
366 <has_text text="Skipping CodingQuarry as no --rna_bam passed"/>
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
367 <has_text text="Running Augustus gene prediction using genus_species parameters"/>
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
368 <not_has_text text="Aligning transcript evidence to genome with minimap2"/>
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
369 <not_has_text text="Found 16 alignments, wrote GFF3 and Augustus hints to file"/>
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
370 <not_has_text text="Extracting hints from RNA-seq BAM file using bam2hints"/>
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
371 <has_text text="Mapping 13 proteins to genome using diamond and exonerate"/>
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
372 <has_text text="Found 4 preliminary alignments --> aligning with exonerate"/>
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
373 </assert_stderr>
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
374 </test>
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
375
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
376 <!-- pre-trained augustus -->
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
377 <test>
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
378 <param name="input" value="genome_masked.fa" />
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
379 <param name="database" value="2021-07-20-120000" />
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
380 <section name="organism">
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
381 <param name="species" value="Genus species" />
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
382 </section>
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
383 <section name="augustus">
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
384 <param name="augustus_species" value="fly" />
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
385 </section>
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
386 <section name="busco">
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
387 <param name="busco_seed_species" value="fly" />
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
388 <param name="busco_db" value="insecta" />
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
389 </section>
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
390 <param name="uglyTestingHack" value="true" />
1
1a59958c1f76 "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents: 0
diff changeset
391 <param name="outputs" value="gbk,tbl,gff3,proteins_fa,mrna_transcripts_fa,cds_transcripts_fa,tbl2asn_error,tbl2asn_report,tbl2asn_validation,stats" />
0
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
392 <!-- non deterministic results, so can't be more precise here -->
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
393 <output name="annot_gbk">
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
394 <assert_contents>
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
395 <has_text text=" TITLE Direct Submission" />
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
396 <has_text text="/locus_tag=&quot;FUN_000001&quot;" />
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
397 </assert_contents>
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
398 </output>
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
399 <output name="annot_tbl">
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
400 <assert_contents>
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
401 <has_text text=">Feature sample" />
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
402 <has_text text="gnl|ncbi|FUN_000001-T1_mrna" />
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
403 </assert_contents>
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
404 </output>
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
405 <output name="annot_gff3">
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
406 <assert_contents>
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
407 <has_text text="##gff-version 3" />
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
408 <has_text text="ID=FUN_000001-T1;Parent=FUN_000001;product=hypothetical protein;" />
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
409 </assert_contents>
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
410 </output>
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
411 <output name="fasta_proteins">
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
412 <assert_contents>
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
413 <has_text text=">FUN_000001-T1 FUN_000001" />
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
414 </assert_contents>
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
415 </output>
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
416 <output name="fasta_transcripts_mrna">
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
417 <assert_contents>
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
418 <has_text text=">FUN_000001-T1 FUN_000001" />
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
419 </assert_contents>
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
420 </output>
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
421 <output name="fasta_transcripts_cds">
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
422 <assert_contents>
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
423 <has_text text=">FUN_000001-T1 FUN_000001" />
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
424 </assert_contents>
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
425 </output>
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
426 <assert_stderr>
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
427 <has_text text="augustus pretrained"/>
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
428 <has_text text="glimmerhmm busco"/>
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
429 <has_text text="snap busco"/>
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
430 <has_text text="Running BUSCO to find conserved gene models for training ab-initio predictors"/>
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
431 <has_text text="Skipping CodingQuarry as no --rna_bam passed"/>
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
432 <has_text text="Running Augustus gene prediction using fly parameters"/>
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
433 <not_has_text text="Aligning transcript evidence to genome with minimap2"/>
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
434 <not_has_text text="Found 16 alignments, wrote GFF3 and Augustus hints to file"/>
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
435 <not_has_text text="Extracting hints from RNA-seq BAM file using bam2hints"/>
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
436 <has_text text="Mapping 13 proteins to genome using diamond and exonerate"/>
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
437 <has_text text="Found 4 preliminary alignments --> aligning with exonerate"/>
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
438 </assert_stderr>
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
439 </test>
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
440
1
1a59958c1f76 "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents: 0
diff changeset
441 <!-- bam and transcripts and proteins -->
0
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
442 <test>
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
443 <param name="input" value="genome_masked.fa" />
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
444 <param name="database" value="2021-07-20-120000" />
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
445 <section name="organism">
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
446 <param name="species" value="Genus species" />
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
447 </section>
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
448 <section name="evidences">
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
449 <param name="rna_bam" value="SRR7458692.bam" />
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
450 <param name="transcript_evidence" value="predict_scratch/Genus_species.mrna-transcripts.fa" />
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
451 <conditional name="prot_evidence">
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
452 <param name="prot_evidence_source" value="custom" />
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
453 <param name="protein_evidence" value="predict_scratch/Genus_species.proteins.fa" />
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
454 </conditional>
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
455 </section>
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
456 <section name="busco">
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
457 <param name="busco_seed_species" value="fly" />
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
458 <param name="busco_db" value="insecta" />
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
459 </section>
1
1a59958c1f76 "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents: 0
diff changeset
460 <section name="augustus">
1a59958c1f76 "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents: 0
diff changeset
461 <param name="min_training_models" value="3" />
1a59958c1f76 "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents: 0
diff changeset
462 </section>
1a59958c1f76 "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents: 0
diff changeset
463 <param name="outputs" value="gbk,tbl,gff3,proteins_fa,mrna_transcripts_fa,cds_transcripts_fa,tbl2asn_error,tbl2asn_report,tbl2asn_validation,stats" />
0
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
464 <!-- non deterministic results, so can't be more precise here -->
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
465 <output name="annot_gbk">
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
466 <assert_contents>
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
467 <has_text text=" TITLE Direct Submission" />
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
468 <has_text text="/locus_tag=&quot;FUN_000001&quot;" />
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
469 </assert_contents>
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
470 </output>
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
471 <output name="annot_tbl">
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
472 <assert_contents>
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
473 <has_text text=">Feature sample" />
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
474 <has_text text="gnl|ncbi|FUN_000001-T1_mrna" />
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
475 </assert_contents>
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
476 </output>
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
477 <output name="annot_gff3">
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
478 <assert_contents>
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
479 <has_text text="##gff-version 3" />
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
480 <has_text text="ID=FUN_000001-T1;Parent=FUN_000001;product=hypothetical protein;" />
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
481 </assert_contents>
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
482 </output>
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
483 <output name="fasta_proteins">
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
484 <assert_contents>
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
485 <has_text text=">FUN_000001-T1 FUN_000001" />
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
486 </assert_contents>
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
487 </output>
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
488 <output name="fasta_transcripts_mrna">
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
489 <assert_contents>
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
490 <has_text text=">FUN_000001-T1 FUN_000001" />
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
491 </assert_contents>
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
492 </output>
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
493 <output name="fasta_transcripts_cds">
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
494 <assert_contents>
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
495 <has_text text=">FUN_000001-T1 FUN_000001" />
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
496 </assert_contents>
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
497 </output>
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
498 <assert_stderr>
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
499 <has_text text="augustus busco"/>
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
500 <has_text text="glimmerhmm busco"/>
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
501 <has_text text="snap busco"/>
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
502 <has_text text="Running BUSCO to find conserved gene models for training ab-initio predictors"/>
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
503 <not_has_text text="Skipping CodingQuarry as no --rna_bam passed"/>
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
504 <has_text text="Running Augustus gene prediction using genus_species parameters"/>
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
505 <has_text text="Training Augustus using BUSCO gene models"/>
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
506 <has_text text="Aligning transcript evidence to genome with minimap2"/>
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
507 <has_text text="Found 16 alignments, wrote GFF3 and Augustus hints to file"/>
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
508 <has_text text="Extracting hints from RNA-seq BAM file using bam2hints"/>
2
33092577d65d "planemo upload commit c70e2e82ba7d3f9ee43c101ab267cdf0847d8864"
iuc
parents: 1
diff changeset
509 <has_text text="Mapping 16 proteins to genome using diamond and exonerate"/>
33092577d65d "planemo upload commit c70e2e82ba7d3f9ee43c101ab267cdf0847d8864"
iuc
parents: 1
diff changeset
510 <has_text text="Found 21 preliminary alignments --> aligning with exonerate"/>
0
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
511 </assert_stderr>
2
33092577d65d "planemo upload commit c70e2e82ba7d3f9ee43c101ab267cdf0847d8864"
iuc
parents: 1
diff changeset
512 <assert_command>
33092577d65d "planemo upload commit c70e2e82ba7d3f9ee43c101ab267cdf0847d8864"
iuc
parents: 1
diff changeset
513 <has_text text="--protein_evidence"/>
33092577d65d "planemo upload commit c70e2e82ba7d3f9ee43c101ab267cdf0847d8864"
iuc
parents: 1
diff changeset
514 </assert_command>
0
40b87aef5241 "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
515 </test>
1
1a59958c1f76 "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents: 0
diff changeset
516
1a59958c1f76 "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents: 0
diff changeset
517 <!-- proteins -->
1a59958c1f76 "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents: 0
diff changeset
518 <test>
1a59958c1f76 "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents: 0
diff changeset
519 <param name="input" value="genome_masked.fa" />
1a59958c1f76 "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents: 0
diff changeset
520 <param name="database" value="2021-07-20-120000" />
1a59958c1f76 "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents: 0
diff changeset
521 <section name="organism">
1a59958c1f76 "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents: 0
diff changeset
522 <param name="species" value="Genus species" />
1a59958c1f76 "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents: 0
diff changeset
523 </section>
1a59958c1f76 "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents: 0
diff changeset
524 <section name="evidences">
1a59958c1f76 "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents: 0
diff changeset
525 <conditional name="prot_evidence">
1a59958c1f76 "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents: 0
diff changeset
526 <param name="prot_evidence_source" value="custom" />
1a59958c1f76 "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents: 0
diff changeset
527 <param name="protein_evidence" value="predict_scratch/Genus_species.proteins.fa" />
1a59958c1f76 "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents: 0
diff changeset
528 </conditional>
1a59958c1f76 "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents: 0
diff changeset
529 </section>
1a59958c1f76 "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents: 0
diff changeset
530 <section name="busco">
1a59958c1f76 "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents: 0
diff changeset
531 <param name="busco_seed_species" value="fly" />
1a59958c1f76 "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents: 0
diff changeset
532 <param name="busco_db" value="insecta" />
1a59958c1f76 "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents: 0
diff changeset
533 </section>
1a59958c1f76 "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents: 0
diff changeset
534 <section name="augustus">
1a59958c1f76 "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents: 0
diff changeset
535 <param name="min_training_models" value="3" />
1a59958c1f76 "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents: 0
diff changeset
536 </section>
1a59958c1f76 "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents: 0
diff changeset
537 <param name="outputs" value="gbk,tbl,gff3,proteins_fa,mrna_transcripts_fa,cds_transcripts_fa,tbl2asn_error,tbl2asn_report,tbl2asn_validation,stats" />
1a59958c1f76 "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents: 0
diff changeset
538 <!-- non deterministic results, so can't be more precise here -->
1a59958c1f76 "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents: 0
diff changeset
539 <output name="annot_gbk">
1a59958c1f76 "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents: 0
diff changeset
540 <assert_contents>
1a59958c1f76 "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents: 0
diff changeset
541 <has_text text=" TITLE Direct Submission" />
1a59958c1f76 "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents: 0
diff changeset
542 <has_text text="/locus_tag=&quot;FUN_000001&quot;" />
1a59958c1f76 "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents: 0
diff changeset
543 </assert_contents>
1a59958c1f76 "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents: 0
diff changeset
544 </output>
1a59958c1f76 "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents: 0
diff changeset
545 <output name="annot_tbl">
1a59958c1f76 "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents: 0
diff changeset
546 <assert_contents>
1a59958c1f76 "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents: 0
diff changeset
547 <has_text text=">Feature sample" />
1a59958c1f76 "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents: 0
diff changeset
548 <has_text text="gnl|ncbi|FUN_000001-T1_mrna" />
1a59958c1f76 "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents: 0
diff changeset
549 </assert_contents>
1a59958c1f76 "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents: 0
diff changeset
550 </output>
1a59958c1f76 "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents: 0
diff changeset
551 <output name="annot_gff3">
1a59958c1f76 "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents: 0
diff changeset
552 <assert_contents>
1a59958c1f76 "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents: 0
diff changeset
553 <has_text text="##gff-version 3" />
1a59958c1f76 "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents: 0
diff changeset
554 <has_text text="ID=FUN_000001-T1;Parent=FUN_000001;product=hypothetical protein;" />
1a59958c1f76 "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents: 0
diff changeset
555 </assert_contents>
1a59958c1f76 "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents: 0
diff changeset
556 </output>
1a59958c1f76 "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents: 0
diff changeset
557 <output name="fasta_proteins">
1a59958c1f76 "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents: 0
diff changeset
558 <assert_contents>
1a59958c1f76 "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents: 0
diff changeset
559 <has_text text=">FUN_000001-T1 FUN_000001" />
1a59958c1f76 "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents: 0
diff changeset
560 </assert_contents>
1a59958c1f76 "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents: 0
diff changeset
561 </output>
1a59958c1f76 "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents: 0
diff changeset
562 <output name="fasta_transcripts_mrna">
1a59958c1f76 "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents: 0
diff changeset
563 <assert_contents>
1a59958c1f76 "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents: 0
diff changeset
564 <has_text text=">FUN_000001-T1 FUN_000001" />
1a59958c1f76 "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents: 0
diff changeset
565 </assert_contents>
1a59958c1f76 "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents: 0
diff changeset
566 </output>
1a59958c1f76 "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents: 0
diff changeset
567 <output name="fasta_transcripts_cds">
1a59958c1f76 "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents: 0
diff changeset
568 <assert_contents>
1a59958c1f76 "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents: 0
diff changeset
569 <has_text text=">FUN_000001-T1 FUN_000001" />
1a59958c1f76 "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents: 0
diff changeset
570 </assert_contents>
1a59958c1f76 "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents: 0
diff changeset
571 </output>
1a59958c1f76 "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents: 0
diff changeset
572 <assert_stderr>
1a59958c1f76 "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents: 0
diff changeset
573 <has_text text="augustus busco"/>
1a59958c1f76 "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents: 0
diff changeset
574 <has_text text="glimmerhmm busco"/>
1a59958c1f76 "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents: 0
diff changeset
575 <has_text text="snap busco"/>
1a59958c1f76 "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents: 0
diff changeset
576 <has_text text="Running BUSCO to find conserved gene models for training ab-initio predictors"/>
1a59958c1f76 "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents: 0
diff changeset
577 <has_text text="Skipping CodingQuarry as no --rna_bam passed"/>
1a59958c1f76 "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents: 0
diff changeset
578 <has_text text="Running Augustus gene prediction using genus_species parameters"/>
1a59958c1f76 "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents: 0
diff changeset
579 <has_text text="Training Augustus using BUSCO gene models"/>
1a59958c1f76 "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents: 0
diff changeset
580 <not_has_text text="Aligning transcript evidence to genome with minimap2"/>
1a59958c1f76 "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents: 0
diff changeset
581 <not_has_text text="Found 16 alignments, wrote GFF3 and Augustus hints to file"/>
1a59958c1f76 "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents: 0
diff changeset
582 <not_has_text text="Extracting hints from RNA-seq BAM file using bam2hints"/>
2
33092577d65d "planemo upload commit c70e2e82ba7d3f9ee43c101ab267cdf0847d8864"
iuc
parents: 1
diff changeset
583 <has_text text="Mapping 16 proteins to genome using diamond and exonerate"/>
33092577d65d "planemo upload commit c70e2e82ba7d3f9ee43c101ab267cdf0847d8864"
iuc
parents: 1
diff changeset
584 <has_text text="Found 21 preliminary alignments --> aligning with exonerate"/>
1
1a59958c1f76 "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents: 0
diff changeset
585 </assert_stderr>
2
33092577d65d "planemo upload commit c70e2e82ba7d3f9ee43c101ab267cdf0847d8864"
iuc
parents: 1
diff changeset
586 <assert_command>
33092577d65d "planemo upload commit c70e2e82ba7d3f9ee43c101ab267cdf0847d8864"
iuc
parents: 1
diff changeset
587 <has_text text="--protein_evidence"/>
33092577d65d "planemo upload commit c70e2e82ba7d3f9ee43c101ab267cdf0847d8864"
iuc
parents: 1
diff changeset
588 </assert_command>
1
1a59958c1f76 "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents: 0
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589 </test>
0
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590 </tests>
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591 <help><![CDATA[
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592 Funannotate_ predict
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593 --------------------
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594
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595 Funannotate_ is a pipeline for genome annotation (built specifically for fungi, but will also work with higher eukaryotes).
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596
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597 Script takes genome multi-fasta file and a variety of inputs to do a comprehensive whole
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598 genome gene prediction. Uses AUGUSTUS, GeneMark, Snap, GlimmerHMM, BUSCO, EVidence Modeler,
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599 tbl2asn, tRNAScan-SE, Exonerate, minimap2.
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600
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601 .. _Funannotate: http://funannotate.readthedocs.io
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602 ]]></help>
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603 <expand macro="citations" />
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604 </tool>