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comparison funannotate_predict.xml @ 13:3e13e35ef26b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate commit 8341270dd36185ebf59d15282bc79f1215e936a4
author iuc
date Fri, 07 Mar 2025 22:35:08 +0000
parents 4b96ced19f75
children
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12:4b96ced19f75 13:3e13e35ef26b
19 #if $uglyTestingHack == "true": 19 #if $uglyTestingHack == "true":
20 ## funannotate_db contains some hard coded path, need to rewrite one for tests (not in real life when using data manager) 20 ## funannotate_db contains some hard coded path, need to rewrite one for tests (not in real life when using data manager)
21 ## Need to copy too as the test_data is read only on CI 21 ## Need to copy too as the test_data is read only on CI
22 cp -r '${database.fields.path}' './hacked_database' && 22 cp -r '${database.fields.path}' './hacked_database' &&
23 sed -i.bak 's|/tmp/prout|'`pwd`'/hacked_database|' './hacked_database/trained_species/fly/info.json' && 23 sed -i.bak 's|/tmp/prout|'`pwd`'/hacked_database|' './hacked_database/trained_species/fly/info.json' &&
24 #end if 24 #set db_path='$(pwd)/hacked_database'
25 #else
26 #set db_path=$database.fields.path
27 #end if
28
29 ## show detailed info about the reference DB on stdout
30 export FUNANNOTATE_DB="$db_path" &&
31 funannotate database &&
25 32
26 mkdir -p input/ && 33 mkdir -p input/ &&
27 ln -s '${input}' input/input.fasta && 34 ln -s '${input}' input/input.fasta &&
28 35
29 funannotate predict 36 funannotate predict
30 --input input/input.fasta 37 --input input/input.fasta
31 --out output 38 --out output
32 --tmpdir "\${_GALAXY_JOB_TMP_DIR:-/tmp}" 39 --tmpdir "\${_GALAXY_JOB_TMP_DIR:-/tmp}"
33 #if $uglyTestingHack == "true": 40 --database "$db_path"
34 --database `pwd`'/hacked_database'
35 #else
36 --database '$database.fields.path'
37 #end if
38 41
39 $force 42 $force
40 43
41 --species '${organism.species}' 44 --species '${organism.species}'
42 --isolate '${organism.isolate}' 45 --isolate '${organism.isolate}'
47 --SeqAccession '${organism.SeqAccession}' 50 --SeqAccession '${organism.SeqAccession}'
48 --name '${organism.name}' 51 --name '${organism.name}'
49 --numbering ${organism.numbering} 52 --numbering ${organism.numbering}
50 --header_length ${header_length} 53 --header_length ${header_length}
51 54
52 #if $parameters: 55 ## #if $parameters:
53 --parameters '${parameters}' 56 ## --parameters '${parameters}'
54 #end if 57 ## #end if
55 58
56 #if $evidences.rna_bam 59 #if $evidences.rna_bam
57 --rna_bam ${evidences.rna_bam} 60 --rna_bam ${evidences.rna_bam}
58 #end if 61 #end if
59 62
79 --p2g_prefilter ${evidences.p2g_prefilter} 82 --p2g_prefilter ${evidences.p2g_prefilter}
80 83
81 --busco_seed_species '${busco.busco_seed_species}' 84 --busco_seed_species '${busco.busco_seed_species}'
82 --busco_db '${busco.busco_db}' 85 --busco_db '${busco.busco_db}'
83 86
84 #if $augustus.augustus_species != 'none': 87 #if $augustus.augustus_species:
85 --augustus_species '${augustus.augustus_species}' 88 --augustus_species '${augustus.augustus_species}'
86 #end if 89 #end if
87 --min_training_models ${augustus.min_training_models} 90 --min_training_models ${augustus.min_training_models}
88 ${augustus.optimize_augustus} 91 ${augustus.optimize_augustus}
89 92
145 <param name="database" label="Funannotate database" type="select"> 148 <param name="database" label="Funannotate database" type="select">
146 <options from_data_table="funannotate"> 149 <options from_data_table="funannotate">
147 <column name="value" index="0" /> 150 <column name="value" index="0" />
148 <column name="name" index="1" /> 151 <column name="name" index="1" />
149 <column name="path" index="3" /> 152 <column name="path" index="3" />
150 <filter type="sort_by" column="0" /> 153 <filter type="sort_by" column="0" reverse_sort_order="true"/>
151 <filter type="static_value" column="2" value="1.0" /> 154 <filter type="static_value" column="2" value="1.0" />
152 </options> 155 </options>
153 </param> 156 </param>
154 157
155 <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" /> 158 <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" />
191 <section name="busco" expanded="true" title="Busco"> 194 <section name="busco" expanded="true" title="Busco">
192 <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)."> 195 <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).">
193 <expand macro="busco_species"/> 196 <expand macro="busco_species"/>
194 </param> 197 </param>
195 <param argument="--busco_seed_species" type="select" label="Initial Augustus species training set for BUSCO alignment" help="Used when BUSCO runs Augustus internally."> 198 <param argument="--busco_seed_species" type="select" label="Initial Augustus species training set for BUSCO alignment" help="Used when BUSCO runs Augustus internally.">
196 <expand macro="augustus_species"/> 199 <expand macro="busco_seeds">
200 <filter type="add_value" value="anidulans" name="Anidulans" index="0"/> <!-- this sets the default -->
201 </expand>
197 </param> 202 </param>
198 </section> 203 </section>
199 204
200 <section name="filtering" expanded="true" title="Filtering"> 205 <section name="filtering" expanded="true" title="Filtering">
201 <param argument="--min_intronlen" type="integer" value="10" label="Minimum intron length" /> 206 <param argument="--min_intronlen" type="integer" value="10" min="0" label="Minimum intron length" />
202 <param argument="--max_intronlen" type="integer" value="3000" label="Maximum intron length" /> 207 <param argument="--max_intronlen" type="integer" value="3000" min="0" label="Maximum intron length" />
203 <param argument="--min_protlen" type="integer" value="50" label="Minimum protein length" /> 208 <param argument="--min_protlen" type="integer" value="50" min="0" label="Minimum protein length" />
204 <param argument="--keep_no_stops" type="boolean" checked="false" truevalue="--keep_no_stops" falsevalue="" label="Keep gene models without valid stops" /> 209 <param argument="--keep_no_stops" type="boolean" checked="false" truevalue="--keep_no_stops" falsevalue="" label="Keep gene models without valid stops" />
205 <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"> 210 <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">
206 <option value="overlap blast" selected="True">overlap + blast</option> 211 <option value="overlap blast" selected="True">overlap + blast</option>
207 <option value="overlap">overlap</option> 212 <option value="overlap">overlap</option>
208 <option value="blast">blast</option> 213 <option value="blast">blast</option>
209 <option value="none">none</option> 214 <option value="none">none</option>
210 </param> 215 </param>
211 </section> 216 </section>
212 217
213 <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." /> 218 <!-- <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." /> -->
214 219
215 <section name="augustus" expanded="false" title="Augustus settings (advanced)"> 220 <section name="augustus" expanded="false" title="Augustus settings (advanced)">
216 <param argument="--augustus_species" type="select" label="Augustus species training set" help="Select a species from the list"> 221 <param argument="--augustus_species" type="select" optional="true" label="Augustus species training set" help="Select a species from the list, use species name if empty">
217 <option value="none" selected="True">No corresponding species, train from scratch</option> 222 <expand macro="busco_seeds"/>
218 <expand macro="augustus_species"/>
219 </param> 223 </param>
220 <param argument="--min_training_models" type="integer" value="200" label="Minimum number of models to train Augustus" /> 224 <param argument="--min_training_models" type="integer" value="200" label="Minimum number of models to train Augustus" />
221 <param argument="--optimize_augustus" type="boolean" checked="false" truevalue="--optimize_augustus" falsevalue="" label="Run 'optimize_augustus.pl' to refine training (long runtime)" /> 225 <param argument="--optimize_augustus" type="boolean" checked="false" truevalue="--optimize_augustus" falsevalue="" label="Run 'optimize_augustus.pl' to refine training (long runtime)" />
222 </section> 226 </section>
223 227