Mercurial > repos > iuc > funannotate_predict
annotate funannotate_predict.xml @ 9:d6c7106b7b2e draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate commit 90acc0e23230b2e29e1d38a90bca4009c84c7e67
author | iuc |
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date | Fri, 20 Oct 2023 10:08:19 +0000 |
parents | 51b6ee65ef7f |
children | 1bc5a03faf2e |
rev | line source |
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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 mkdir -p input/ && |
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26 ln -s '${input}' input/input.fasta && |
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27 |
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28 funannotate predict |
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29 --input input/input.fasta |
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30 --out output |
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31 #if $uglyTestingHack == "true": |
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32 --database `pwd`'/hacked_database' |
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33 #else |
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34 --database '$database.fields.path' |
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35 #end if |
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36 |
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37 $force |
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38 |
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39 --species '${organism.species}' |
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40 --isolate '${organism.isolate}' |
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41 --strain '${organism.strain}' |
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42 --organism '${organism.organism}' |
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43 --ploidy ${organism.ploidy} |
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44 --SeqCenter '${organism.SeqCenter}' |
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45 --SeqAccession '${organism.SeqAccession}' |
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46 --name '${organism.name}' |
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47 --numbering ${organism.numbering} |
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48 |
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49 #if $parameters: |
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50 --parameters '${parameters}' |
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51 #end if |
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52 |
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53 #if $evidences.rna_bam |
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54 --rna_bam ${evidences.rna_bam} |
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55 #end if |
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56 |
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57 #set est_list = "" |
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58 #if len($evidences.transcript_evidence) > 0: |
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59 #for $estev in $evidences.transcript_evidence: |
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60 #if $estev: |
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61 #set est_list += " '" + str($estev) + "'" |
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62 #end if |
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63 #end for |
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64 #end if |
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65 #if $est_list: |
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66 --transcript_evidence $est_list |
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67 #end if |
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68 |
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69 #if $evidences.prot_evidence.prot_evidence_source == 'custom': |
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70 --protein_evidence |
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71 #for $protev in $evidences.prot_evidence.protein_evidence: |
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72 '${protev}' |
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73 #end for |
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74 #end if |
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75 --p2g_pident ${evidences.p2g_pident} |
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76 --p2g_prefilter ${evidences.p2g_prefilter} |
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77 |
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78 --busco_seed_species '${busco.busco_seed_species}' |
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79 --busco_db '${busco.busco_db}' |
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80 |
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81 #if $augustus.augustus_species != 'none': |
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82 --augustus_species '${augustus.augustus_species}' |
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83 #end if |
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84 --min_training_models ${augustus.min_training_models} |
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85 ${augustus.optimize_augustus} |
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86 |
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87 #if $genemark.genemark_license: |
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88 --genemark_mode '${genemark.genemark_mode}' |
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89 #if $genemark.genemark_mod: |
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90 --genemark_mod '${genemark.genemark_mod}' |
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91 #end if |
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92 --soft_mask ${genemark.soft_mask} |
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93 #end if |
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94 |
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95 $evm.repeats2evm |
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96 #if $evm.evm_partitioning.evm_partition == "yes": |
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97 --evm-partition-interval ${evm.evm_partitioning.evm_partition_interval} |
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98 #else: |
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99 --no-evm-partitions |
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100 #end if |
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101 #if $evm.weights: |
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102 --weights '${evm.weights}' |
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103 #end if |
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104 |
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105 #if $other_predictors.stringtie: |
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106 --stringtie '${other_predictors.stringtie}' |
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107 #end if |
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108 #if $other_predictors.maker_gff: |
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109 --maker_gff '${other_predictors.maker_gff}' |
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110 #end if |
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111 #if $other_predictors.pasa_gff: |
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112 --pasa_gff '${other_predictors.pasa_gff}:${other_predictors.pasa_gff_weight}' |
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113 #end if |
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114 #if $other_predictors.other_gff: |
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115 --other_gff '${other_predictors.other_gff}:${other_predictors.other_gff_weight}' |
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116 #end if |
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117 |
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118 --min_intronlen ${filtering.min_intronlen} |
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119 --max_intronlen ${filtering.max_intronlen} |
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120 --min_protlen ${filtering.min_protlen} |
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121 ${filtering.keep_no_stops} |
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122 --repeat_filter ${filtering.repeat_filter} |
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123 |
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124 --cpus \${GALAXY_SLOTS:-2} |
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125 |
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126 && |
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127 |
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128 mv output/predict_results/*.gbk out.gbk && |
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129 mv output/predict_results/*.tbl out.tbl && |
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130 mv output/predict_results/*.gff3 out.gff3 && |
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131 mv output/predict_results/*.proteins.fa out.proteins.fa && |
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132 mv output/predict_results/*.mrna-transcripts.fa out.mrna-transcripts.fa && |
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133 mv output/predict_results/*.cds-transcripts.fa out.cds-transcripts.fa && |
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134 mv output/predict_results/*.discrepency.report.txt out.discrepency.report.txt && |
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135 mv output/predict_results/*.error.summary.txt out.error.summary.txt && |
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136 mv output/predict_results/*.validation.txt out.validation.txt && |
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137 mv output/predict_results/*.stats.json out.stats.json |
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138 ]]></command> |
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139 <inputs> |
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140 <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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141 |
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142 <param name="database" label="Funannotate database" type="select"> |
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143 <options from_data_table="funannotate"> |
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144 <column name="value" index="0" /> |
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145 <column name="name" index="1" /> |
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146 <column name="path" index="3" /> |
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147 <filter type="sort_by" column="0" /> |
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148 <filter type="static_value" column="2" value="1.0" /> |
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149 </options> |
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150 </param> |
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151 |
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152 <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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153 |
0
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154 <section name="organism" expanded="true" title="Organism"> |
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155 <param argument="--species" type="text" optional="false" label="Name of the species to annotate" help="e.g. Genus species"> |
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156 <validator type="empty_field" /> |
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157 </param> |
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158 <param argument="--isolate" type="text" label="Isolate name" help="If relevant (e.g. Af293)" /> |
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159 <param argument="--strain" type="text" label="Strain name" help="If relevant (e.g. FGSCA4)" /> |
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160 <param argument="--organism" type="boolean" checked="false" truevalue="fungus" falsevalue="other" label="Is it a fungus species?" /> |
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161 <param argument="--ploidy" type="integer" value="1" label="Ploidy of assembly" /> |
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162 <param argument="--SeqCenter" type="text" value="CFMR" label="Sequencing facility for NCBI tbl file" /> |
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163 <param argument="--SeqAccession" type="text" value="12345" label="Sequence accession number for NCBI tbl file" /> |
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164 <param argument="--name" type="text" value="FUN_" label="Locus tag prefix" help="Will prefix all the gene names" /> |
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165 <param argument="--numbering" type="integer" value="1" label="Specify where gene numbering starts" /> |
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166 </section> |
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167 |
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168 <section name="evidences" expanded="true" title="Evidences"> |
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169 <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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170 <param argument="--transcript_evidence" type="data" format="fasta" multiple="true" optional="true" label="mRNA/ESTs to align to genome" /> |
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171 <conditional name="prot_evidence"> |
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172 <param name="prot_evidence_source" type="select" label="Select protein evidences"> |
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173 <option value="uniprot" selected="True">Use UniProtKb/SwissProt (from selected Funannotate database)</option> |
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174 <option value="custom">Custom protein sequences</option> |
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175 </param> |
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176 <when value="uniprot"/> |
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177 <when value="custom"> |
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178 <param argument="--protein_evidence" type="data" format="fasta" multiple="true" label="Proteins to map to genome" /> |
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179 </when> |
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180 </conditional> |
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181 <param argument="--p2g_pident" type="integer" value="80" label="Exonerate percent identity (for proteins)" /> |
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182 <param argument="--p2g_prefilter" type="select" label="Prefilter hits with (for proteins)"> |
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183 <option value="diamond" selected="True">Diamond</option> |
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184 <option value="tblastn">tblastn (slower)</option> |
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185 </param> |
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186 </section> |
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187 |
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188 <section name="busco" expanded="true" title="Busco"> |
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189 <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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190 <expand macro="busco_species"/> |
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191 </param> |
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192 <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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193 <expand macro="augustus_species"/> |
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194 </param> |
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195 </section> |
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196 |
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197 <section name="filtering" expanded="true" title="Filtering"> |
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198 <param argument="--min_intronlen" type="integer" value="10" label="Minimum intron length" /> |
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199 <param argument="--max_intronlen" type="integer" value="3000" label="Maximum intron length" /> |
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200 <param argument="--min_protlen" type="integer" value="50" label="Minimum protein length" /> |
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201 <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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202 <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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203 <option value="overlap blast" selected="True">overlap + blast</option> |
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204 <option value="overlap">overlap</option> |
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205 <option value="blast">blast</option> |
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206 <option value="none">none</option> |
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207 </param> |
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208 </section> |
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209 |
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210 <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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211 |
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212 <section name="augustus" expanded="false" title="Augustus settings (advanced)"> |
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213 <param argument="--augustus_species" type="select" label="Augustus species training set" help="Select a species from the list"> |
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214 <option value="none" selected="True">No corresponding species, train from scratch</option> |
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215 <expand macro="augustus_species"/> |
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216 </param> |
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217 <param argument="--min_training_models" type="integer" value="200" label="Minimum number of models to train Augustus" /> |
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218 <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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219 </section> |
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220 |
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221 <section name="genemark" expanded="false" title="GeneMark settings (advanced)"> |
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222 <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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223 <param argument="--genemark_mode" type="select" label="GeneMark mode"> |
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224 <option value="ES" selected="True">ES</option> |
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225 <option value="ET">ET</option> |
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226 </param> |
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227 <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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228 <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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229 </section> |
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230 |
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231 <section name="other_predictors" expanded="false" title="Other annotations (advanced)"> |
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232 <param argument="--stringtie" type="data" format="gtf" optional="true" label="StringTie GTF result" /> |
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233 <param argument="--maker_gff" type="data" format="gff3" optional="true" label="MAKER2 GFF file" help="Parse results directly to EVM" /> |
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234 <param argument="--pasa_gff" type="data" format="gff3" optional="true" label="PASA generated gene models" /> |
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235 <param name="pasa_gff_weight" type="integer" value="1" label="Weight for PASA generated gene models" /> |
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236 <param argument="--other_gff" type="data" format="gff3" optional="true" label="Annotation pass-through to EVM" /> |
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237 <param name="other_gff_weight" type="integer" value="1" label="Weight for annotation pass-through to EVM" /> |
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238 </section> |
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239 |
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240 <section name="evm" expanded="false" title="EVM settings (advanced)"> |
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241 <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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242 <conditional name="evm_partitioning"> |
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243 <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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244 <option value="yes" selected="True">Yes</option> |
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245 <option value="no">No</option> |
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246 </param> |
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247 <when value="yes"> |
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248 <param argument="--evm-partition-interval" type="integer" value="1500" label="Min length between genes to make a partition" /> |
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249 </when> |
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250 <when value="no"/> |
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251 </conditional> |
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252 <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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253 <validator type="regex" message="Key must consist of alphanumeric characters only, possibly separated by the period character ('.')">^[\w: ]+$</validator> |
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254 </param> |
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255 </section> |
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256 |
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257 <param name="outputs" type="select" optional="true" multiple="true" label="Which outputs should be generated"> |
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258 <option value="gbk" selected="true">Annotated genome (genbank)</option> |
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259 <option value="tbl">NCBI tbl annotation file (use for NCBI submission)</option> |
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260 <option value="gff3">Annotation in GFF3 format</option> |
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261 <option value="proteins_fa">Multi-fasta file of protein coding genes</option> |
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262 <option value="mrna_transcripts_fa">Multi-fasta file of transcripts (mRNA)</option> |
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263 <option value="cds_transcripts_fa">Multi-fasta file of transcripts (CDS)</option> |
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264 <option value="tbl2asn_report">tbl2asn summary report of annotated genome</option> |
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265 <option value="tbl2asn_error">tbl2asn error summary report</option> |
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266 <option value="tbl2asn_validation">tbl2asn genome validation report</option> |
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267 <option value="stats">statistics</option> |
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268 </param> |
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269 |
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270 <!-- Need this to change path in the test funannotate_db --> |
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271 <param type="hidden" name="uglyTestingHack" value="" /> |
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272 </inputs> |
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273 <outputs> |
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274 <data name='annot_gbk' format='genbank' label="${tool.name} on ${on_string}: annotation (genbank)" from_work_dir="out.gbk"> |
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275 <filter>outputs and 'gbk' in outputs</filter> |
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276 </data> |
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277 <data name='annot_tbl' format='txt' label="${tool.name} on ${on_string}: NCBI tbl annotation file" from_work_dir="out.tbl"> |
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278 <filter>outputs and 'tbl' in outputs</filter> |
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279 </data> |
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280 <data name='annot_gff3' format='gff3' label="${tool.name} on ${on_string}: annotation (GFF3)" from_work_dir="out.gff3"> |
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281 <filter>outputs and 'gff3' in outputs</filter> |
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282 </data> |
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283 <data name='fasta_proteins' format='fasta' label="${tool.name} on ${on_string}: protein sequences" from_work_dir="out.proteins.fa"> |
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284 <filter>outputs and 'proteins_fa' in outputs</filter> |
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285 </data> |
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286 <data name='fasta_transcripts_mrna' format='fasta' label="${tool.name} on ${on_string}: transcript mRNA sequences" from_work_dir="out.mrna-transcripts.fa"> |
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287 <filter>outputs and 'mrna_transcripts_fa' in outputs</filter> |
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288 </data> |
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289 <data name='fasta_transcripts_cds' format='fasta' label="${tool.name} on ${on_string}: transcript CDS sequences" from_work_dir="out.cds-transcripts.fa"> |
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290 <filter>outputs and 'cds_transcripts_fa' in outputs</filter> |
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291 </data> |
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292 <data name='tbl2asn_report' format='txt' label="${tool.name} on ${on_string}: tbl2asn summary report of annotated genome" from_work_dir="out.discrepency.report.txt"> |
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293 <filter>outputs and 'tbl2asn_report' in outputs</filter> |
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294 </data> |
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295 <data name='tbl2asn_error' format='txt' label="${tool.name} on ${on_string}: tbl2asn error summary report" from_work_dir="out.error.summary.txt"> |
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296 <filter>outputs and 'tbl2asn_error' in outputs</filter> |
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297 </data> |
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298 <data name='tbl2asn_validation' format='txt' label="${tool.name} on ${on_string}: tbl2asn genome validation report" from_work_dir="out.validation.txt"> |
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299 <filter>outputs and 'tbl2asn_validation' in outputs</filter> |
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300 </data> |
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301 <data name='stats' format='json' label="${tool.name} on ${on_string}: stats" from_work_dir="out.stats.json"> |
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302 <filter>outputs and 'stats' in outputs</filter> |
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303 </data> |
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304 <!-- TODO some day: provide trained models as output, reusable as input to other funannotate runs |
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305 (parameters.json file references files with absolute paths, would probably need to create an archive + edit paths in parameters.json) --> |
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306 <!--data name='abinitio' format='json' label="${tool.name} on ${on_string}: ab-initio training parameters" from_work_dir="output/predict_results/*.parameters.json" /--> |
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307 </outputs> |
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308 <tests> |
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309 <!-- training from scratch --> |
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310 <test expect_num_outputs="10"> |
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311 <param name="input" value="genome_masked.fa" /> |
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312 <param name="database" value="2021-07-20-120000" /> |
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313 <section name="busco"> |
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314 <param name="busco_seed_species" value="fly" /> |
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315 <param name="busco_db" value="insecta" /> |
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316 </section> |
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317 <section name="organism"> |
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318 <param name="species" value="Genus species" /> |
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319 </section> |
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320 <section name="augustus"> |
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321 <param name="min_training_models" value="3" /> |
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322 </section> |
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323 <param name="outputs" value="gbk,tbl,gff3,proteins_fa,mrna_transcripts_fa,cds_transcripts_fa,tbl2asn_error,tbl2asn_report,tbl2asn_validation,stats" /> |
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324 <!-- non deterministic results, so can't be more precise here --> |
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325 <output name="annot_gbk"> |
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326 <assert_contents> |
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327 <has_text text=" TITLE Direct Submission" /> |
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328 <has_text text="/locus_tag="FUN_000001"" /> |
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329 </assert_contents> |
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330 </output> |
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331 <output name="annot_tbl"> |
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332 <assert_contents> |
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333 <has_text text=">Feature sample" /> |
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334 <has_text text="gnl|ncbi|FUN_000001-T1_mrna" /> |
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335 </assert_contents> |
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336 </output> |
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337 <output name="annot_gff3"> |
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338 <assert_contents> |
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339 <has_text text="##gff-version 3" /> |
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340 <has_text text="ID=FUN_000001-T1;Parent=FUN_000001;product=hypothetical protein;" /> |
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341 </assert_contents> |
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342 </output> |
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343 <output name="fasta_proteins"> |
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344 <assert_contents> |
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345 <has_text text=">FUN_000001-T1 FUN_000001" /> |
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346 </assert_contents> |
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347 </output> |
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348 <output name="fasta_transcripts_mrna"> |
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349 <assert_contents> |
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350 <has_text text=">FUN_000001-T1 FUN_000001" /> |
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351 </assert_contents> |
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352 </output> |
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353 <output name="fasta_transcripts_cds"> |
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354 <assert_contents> |
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355 <has_text text=">FUN_000001-T1 FUN_000001" /> |
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356 </assert_contents> |
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357 </output> |
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358 <!--output name="abinitio" file="predict_scratch/fly.parameters.json" compare="sim_size" /--> |
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359 <output name="tbl2asn_report" file="predict_scratch/Genus_species.discrepency.report.txt" compare="sim_size" /> |
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360 <output name="tbl2asn_error" file="predict_scratch/Genus_species.error.summary.txt" compare="sim_size" delta="500" /> |
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361 <output name="tbl2asn_validation" file="predict_scratch/Genus_species.validation.txt" compare="sim_size" delta="500" /> |
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362 <output name="stats" file="predict_scratch/Genus_species.stats.json" compare="sim_size" /> |
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363 <assert_stderr> |
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364 <has_text text="augustus busco"/> |
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365 <has_text text="glimmerhmm busco"/> |
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366 <has_text text="snap busco"/> |
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367 <has_text text="Running BUSCO to find conserved gene models for training ab-initio predictors"/> |
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368 <has_text text="Skipping CodingQuarry as no --rna_bam passed"/> |
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369 <has_text text="Running Augustus gene prediction using genus_species parameters"/> |
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370 <not_has_text text="Aligning transcript evidence to genome with minimap2"/> |
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371 <not_has_text text="Found 16 alignments, wrote GFF3 and Augustus hints to file"/> |
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372 <not_has_text text="Extracting hints from RNA-seq BAM file using bam2hints"/> |
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373 <has_text text="Mapping 13 proteins to genome using diamond and exonerate"/> |
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374 <has_text text="Found 4 preliminary alignments with diamond"/> |
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375 </assert_stderr> |
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376 </test> |
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377 |
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378 <!-- pre-trained augustus --> |
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379 <test expect_num_outputs="10"> |
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380 <param name="input" value="genome_masked.fa" /> |
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381 <param name="database" value="2021-07-20-120000" /> |
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382 <section name="organism"> |
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383 <param name="species" value="Genus species" /> |
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384 </section> |
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385 <section name="augustus"> |
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386 <param name="augustus_species" value="fly" /> |
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387 </section> |
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388 <section name="busco"> |
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389 <param name="busco_seed_species" value="fly" /> |
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390 <param name="busco_db" value="insecta" /> |
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391 </section> |
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392 <param name="uglyTestingHack" value="true" /> |
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393 <param name="outputs" value="gbk,tbl,gff3,proteins_fa,mrna_transcripts_fa,cds_transcripts_fa,tbl2asn_error,tbl2asn_report,tbl2asn_validation,stats" /> |
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394 <!-- non deterministic results, so can't be more precise here --> |
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395 <output name="annot_gbk"> |
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396 <assert_contents> |
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397 <has_text text=" TITLE Direct Submission" /> |
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398 <has_text text="/locus_tag="FUN_000001"" /> |
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399 </assert_contents> |
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400 </output> |
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401 <output name="annot_tbl"> |
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402 <assert_contents> |
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403 <has_text text=">Feature sample" /> |
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404 <has_text text="gnl|ncbi|FUN_000001-T1_mrna" /> |
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405 </assert_contents> |
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406 </output> |
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407 <output name="annot_gff3"> |
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408 <assert_contents> |
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409 <has_text text="##gff-version 3" /> |
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410 <has_text text="ID=FUN_000001-T1;Parent=FUN_000001;product=hypothetical protein;" /> |
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411 </assert_contents> |
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412 </output> |
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413 <output name="fasta_proteins"> |
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414 <assert_contents> |
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415 <has_text text=">FUN_000001-T1 FUN_000001" /> |
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416 </assert_contents> |
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417 </output> |
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418 <output name="fasta_transcripts_mrna"> |
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419 <assert_contents> |
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420 <has_text text=">FUN_000001-T1 FUN_000001" /> |
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421 </assert_contents> |
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422 </output> |
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423 <output name="fasta_transcripts_cds"> |
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424 <assert_contents> |
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425 <has_text text=">FUN_000001-T1 FUN_000001" /> |
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426 </assert_contents> |
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427 </output> |
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428 <assert_stderr> |
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429 <has_text text="augustus pretrained"/> |
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430 <has_text text="glimmerhmm busco"/> |
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431 <has_text text="snap busco"/> |
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432 <has_text text="Running BUSCO to find conserved gene models for training ab-initio predictors"/> |
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433 <has_text text="Skipping CodingQuarry as no --rna_bam passed"/> |
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434 <has_text text="Running Augustus gene prediction using fly parameters"/> |
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435 <not_has_text text="Aligning transcript evidence to genome with minimap2"/> |
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436 <not_has_text text="Found 16 alignments, wrote GFF3 and Augustus hints to file"/> |
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437 <not_has_text text="Extracting hints from RNA-seq BAM file using bam2hints"/> |
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438 <has_text text="Mapping 13 proteins to genome using diamond and exonerate"/> |
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51b6ee65ef7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate commit 2589d2785ca90160a22a5fe14e03311e189ea51d
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439 <has_text text="Found 4 preliminary alignments with diamond"/> |
0
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440 </assert_stderr> |
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441 </test> |
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442 |
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443 <!-- bam and transcripts and proteins --> |
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d6c7106b7b2e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate commit 90acc0e23230b2e29e1d38a90bca4009c84c7e67
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444 <test expect_num_outputs="10"> |
0
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445 <param name="input" value="genome_masked.fa" /> |
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446 <param name="database" value="2021-07-20-120000" /> |
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447 <section name="organism"> |
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448 <param name="species" value="Genus species" /> |
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449 </section> |
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450 <section name="evidences"> |
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451 <param name="rna_bam" value="SRR7458692.bam" /> |
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452 <param name="transcript_evidence" value="predict_scratch/Genus_species.mrna-transcripts.fa" /> |
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453 <conditional name="prot_evidence"> |
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454 <param name="prot_evidence_source" value="custom" /> |
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455 <param name="protein_evidence" value="predict_scratch/Genus_species.proteins.fa" /> |
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456 </conditional> |
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457 </section> |
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458 <section name="busco"> |
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459 <param name="busco_seed_species" value="fly" /> |
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460 <param name="busco_db" value="insecta" /> |
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461 </section> |
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462 <section name="augustus"> |
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463 <param name="min_training_models" value="3" /> |
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464 </section> |
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465 <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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466 <!-- non deterministic results, so can't be more precise here --> |
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467 <output name="annot_gbk"> |
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468 <assert_contents> |
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469 <has_text text=" TITLE Direct Submission" /> |
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470 <has_text text="/locus_tag="FUN_000001"" /> |
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471 </assert_contents> |
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472 </output> |
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473 <output name="annot_tbl"> |
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474 <assert_contents> |
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475 <has_text text=">Feature sample" /> |
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476 <has_text text="gnl|ncbi|FUN_000001-T1_mrna" /> |
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477 </assert_contents> |
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478 </output> |
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479 <output name="annot_gff3"> |
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480 <assert_contents> |
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481 <has_text text="##gff-version 3" /> |
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482 <has_text text="ID=FUN_000001-T1;Parent=FUN_000001;product=hypothetical protein;" /> |
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483 </assert_contents> |
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484 </output> |
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485 <output name="fasta_proteins"> |
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486 <assert_contents> |
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487 <has_text text=">FUN_000001-T1 FUN_000001" /> |
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488 </assert_contents> |
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489 </output> |
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490 <output name="fasta_transcripts_mrna"> |
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491 <assert_contents> |
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492 <has_text text=">FUN_000001-T1 FUN_000001" /> |
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493 </assert_contents> |
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494 </output> |
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495 <output name="fasta_transcripts_cds"> |
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496 <assert_contents> |
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497 <has_text text=">FUN_000001-T1 FUN_000001" /> |
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498 </assert_contents> |
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499 </output> |
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500 <assert_stderr> |
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501 <has_text text="augustus busco"/> |
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502 <has_text text="glimmerhmm busco"/> |
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503 <has_text text="snap busco"/> |
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504 <has_text text="Running BUSCO to find conserved gene models for training ab-initio predictors"/> |
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505 <not_has_text text="Skipping CodingQuarry as no --rna_bam passed"/> |
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506 <has_text text="Running Augustus gene prediction using genus_species parameters"/> |
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507 <has_text text="Training Augustus using BUSCO gene models"/> |
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508 <has_text text="Aligning transcript evidence to genome with minimap2"/> |
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509 <has_text text="Found 16 alignments, wrote GFF3 and Augustus hints to file"/> |
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510 <has_text text="Extracting hints from RNA-seq BAM file using bam2hints"/> |
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iuc
parents:
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511 <has_text text="Mapping 16 proteins to genome using diamond and exonerate"/> |
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51b6ee65ef7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate commit 2589d2785ca90160a22a5fe14e03311e189ea51d
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512 <has_text text="Found 21 preliminary alignments with diamond"/> |
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513 </assert_stderr> |
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514 <assert_command> |
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515 <has_text text="--protein_evidence"/> |
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516 </assert_command> |
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517 </test> |
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518 |
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519 <!-- proteins --> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate commit 90acc0e23230b2e29e1d38a90bca4009c84c7e67
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520 <test expect_num_outputs="10"> |
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521 <param name="input" value="genome_masked.fa" /> |
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522 <param name="database" value="2021-07-20-120000" /> |
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523 <section name="organism"> |
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524 <param name="species" value="Genus species" /> |
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525 </section> |
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526 <section name="evidences"> |
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527 <conditional name="prot_evidence"> |
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528 <param name="prot_evidence_source" value="custom" /> |
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529 <param name="protein_evidence" value="predict_scratch/Genus_species.proteins.fa" /> |
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530 </conditional> |
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531 </section> |
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532 <section name="busco"> |
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533 <param name="busco_seed_species" value="fly" /> |
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534 <param name="busco_db" value="insecta" /> |
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535 </section> |
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536 <section name="augustus"> |
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537 <param name="min_training_models" value="3" /> |
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538 </section> |
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539 <param name="outputs" value="gbk,tbl,gff3,proteins_fa,mrna_transcripts_fa,cds_transcripts_fa,tbl2asn_error,tbl2asn_report,tbl2asn_validation,stats" /> |
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540 <!-- non deterministic results, so can't be more precise here --> |
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541 <output name="annot_gbk"> |
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542 <assert_contents> |
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543 <has_text text=" TITLE Direct Submission" /> |
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544 <has_text text="/locus_tag="FUN_000001"" /> |
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545 </assert_contents> |
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546 </output> |
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547 <output name="annot_tbl"> |
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548 <assert_contents> |
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549 <has_text text=">Feature sample" /> |
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550 <has_text text="gnl|ncbi|FUN_000001-T1_mrna" /> |
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551 </assert_contents> |
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552 </output> |
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553 <output name="annot_gff3"> |
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554 <assert_contents> |
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555 <has_text text="##gff-version 3" /> |
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556 <has_text text="ID=FUN_000001-T1;Parent=FUN_000001;product=hypothetical protein;" /> |
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557 </assert_contents> |
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558 </output> |
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559 <output name="fasta_proteins"> |
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560 <assert_contents> |
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561 <has_text text=">FUN_000001-T1 FUN_000001" /> |
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562 </assert_contents> |
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563 </output> |
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564 <output name="fasta_transcripts_mrna"> |
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565 <assert_contents> |
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566 <has_text text=">FUN_000001-T1 FUN_000001" /> |
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567 </assert_contents> |
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568 </output> |
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569 <output name="fasta_transcripts_cds"> |
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570 <assert_contents> |
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571 <has_text text=">FUN_000001-T1 FUN_000001" /> |
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572 </assert_contents> |
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573 </output> |
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574 <assert_stderr> |
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575 <has_text text="augustus busco"/> |
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576 <has_text text="glimmerhmm busco"/> |
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577 <has_text text="snap busco"/> |
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578 <has_text text="Running BUSCO to find conserved gene models for training ab-initio predictors"/> |
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579 <has_text text="Skipping CodingQuarry as no --rna_bam passed"/> |
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580 <has_text text="Running Augustus gene prediction using genus_species parameters"/> |
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581 <has_text text="Training Augustus using BUSCO gene models"/> |
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582 <not_has_text text="Aligning transcript evidence to genome with minimap2"/> |
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583 <not_has_text text="Found 16 alignments, wrote GFF3 and Augustus hints to file"/> |
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584 <not_has_text text="Extracting hints from RNA-seq BAM file using bam2hints"/> |
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585 <has_text text="Mapping 16 proteins to genome using diamond and exonerate"/> |
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586 <has_text text="Found 21 preliminary alignments with diamond"/> |
1
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587 </assert_stderr> |
2
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588 <assert_command> |
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589 <has_text text="--protein_evidence"/> |
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590 </assert_command> |
1
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591 </test> |
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592 </tests> |
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593 <help><![CDATA[ |
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594 Funannotate_ predict |
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595 -------------------- |
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596 |
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597 Funannotate_ is a pipeline for genome annotation (built specifically for fungi, but will also work with higher eukaryotes). |
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598 |
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599 Script takes genome multi-fasta file and a variety of inputs to do a comprehensive whole |
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600 genome gene prediction. Uses AUGUSTUS, GeneMark, Snap, GlimmerHMM, BUSCO, EVidence Modeler, |
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601 tbl2asn, tRNAScan-SE, Exonerate, minimap2. |
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602 |
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603 .. _Funannotate: http://funannotate.readthedocs.io |
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604 ]]></help> |
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605 <expand macro="citations" /> |
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606 </tool> |