Mercurial > repos > iuc > busco

comparison busco.xml @ 7:4048d82f0c88 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload commit 22186dcfbe33d17fabd4a3c4fa39d4313978fc9c"
author iuc
date Mon, 17 Aug 2020 06:50:18 -0400
parents 1e62c28ba91d
children 602fb8e63aa7
comparison
equal deleted inserted replaced
6:1e62c28ba91d 7:4048d82f0c88
1 <tool id="busco" name="Busco" profile="18.01" version="@TOOL_VERSION@+galaxy2"> 1 <tool id="busco" name="Busco" profile="18.01" version="@TOOL_VERSION@">
2 <description>assess genome assembly and annotation completeness</description> 2 <description>assess genome assembly and annotation completeness</description>
3 <macros> 3 <macros>
4 <token name="@TOOL_VERSION@">3.0.2</token> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <requirements> 6 <requirements>
7 <requirement type="package" version="@TOOL_VERSION@">busco</requirement> 7 <requirement type="package" version="@TOOL_VERSION@">busco</requirement>
8 <requirement type="package" version="3.5.1">r-base</requirement> 8 <requirement type="package" version="1.32">tar</requirement>
9 <requirement type="package" version="3.3.2">augustus</requirement>
10 <requirement type="package" version="1.29">tar</requirement>
11 </requirements> 9 </requirements>
12 <command><![CDATA[ 10 <command><![CDATA[
13 export BUSCO_CONFIG_FILE='busco_config.ini' && 11 if [ -z "\$AUGUSTUS_CONFIG_PATH" ] ; then BUSCO_PATH=\$(dirname \$(which busco)) ; export AUGUSTUS_CONFIG_PATH=\$(realpath \${BUSCO_PATH}/../config) ; fi &&
14 if [ -z "\$AUGUSTUS_CONFIG_PATH" ] ; then BUSCO_PATH=\$(dirname \$(which run_BUSCO.py)) ; export AUGUSTUS_CONFIG_PATH=\$(realpath \${BUSCO_PATH}/../config) ; fi &&
15 cp -r "\$AUGUSTUS_CONFIG_PATH/" augustus_dir/ && 12 cp -r "\$AUGUSTUS_CONFIG_PATH/" augustus_dir/ &&
16 export AUGUSTUS_CONFIG_PATH=`pwd`/augustus_dir/ && 13 export AUGUSTUS_CONFIG_PATH=`pwd`/augustus_dir/ &&
17 14
18 #if $adv.aug_prediction.augustus_mode == 'history': 15 #if $adv.aug_prediction.augustus_mode == 'history':
19 ## Using an augustus model from history, we need to unzip it and let augustus find it 16 ## Using an augustus model from history, we need to unzip it and let augustus find it
20 mkdir -p 'augustus_dir/species/' && 17 mkdir -p 'augustus_dir/species/' &&
21 tar -C 'augustus_dir/species/' -xzf '${adv.aug_prediction.augustus_model}' && 18 tar -C 'augustus_dir/species/' -xzf '${adv.aug_prediction.augustus_model}' &&
22 #end if 19 #end if
23 20
24 run_BUSCO.py 21 busco
25 --in '${input}' 22 --in '${input}'
26 --lineage_path '${lineage_path.fields.path}/${lineage_path.fields.value}' 23 --lineage_dataset '${lineage_dataset}'
24 --update-data
27 --mode '${mode}' 25 --mode '${mode}'
28 -o busco_galaxy 26 -o busco_galaxy
29 --cpu \${GALAXY_SLOTS:-4} 27 --cpu \${GALAXY_SLOTS:-4}
30 --evalue ${adv.evalue} 28 --evalue ${adv.evalue}
31 ${adv.long} 29 ${adv.long}
32 --limit ${adv.limit} 30 --limit ${adv.limit}
33 #if $adv.aug_prediction.augustus_mode == 'builtin': 31 #if $adv.aug_prediction.augustus_mode == 'builtin':
34 --species '${adv.aug_prediction.augustus_species}' 32 --augustus_species '${adv.aug_prediction.augustus_species}'
35 #else if $adv.aug_prediction.augustus_mode == 'history': 33 #else if $adv.aug_prediction.augustus_mode == 'history':
36 --species local 34 --augustus_species local
37 #end if 35 #end if
38 --tarzip
39 ]]></command> 36 ]]></command>
40 37
41 <inputs> 38 <inputs>
42 <param type="data" name="input" format="fasta" label="Sequences to analyse" help="genome, transcriptome or proteome" /> 39 <param type="data" name="input" format="fasta" label="Sequences to analyse" help="genome, transcriptome or proteome" />
43 <param argument="--mode" type="select" label="Mode"> 40 <param argument="--mode" type="select" label="Mode">
44 <option value="geno">Genome</option> 41 <option value="geno">Genome</option>
45 <option value="tran">Transcriptome</option> 42 <option value="tran">Transcriptome</option>
46 <option value="prot">Proteome</option> 43 <option value="prot">Proteome</option>
47 </param> 44 </param>
48 45
49 <param argument="--lineage_path" type="select" label="Lineage"> 46 <param argument="--lineage_dataset" type="select" label="Lineage">
50 <options from_data_table="busco"> 47 <expand macro="lineages"/>
51 <filter type="sort_by" column="2" />
52 <validator type="no_options" message="No indexes are available" />
53 </options>
54 </param> 48 </param>
55 49
56 <section name="adv" title="Advanced Options" expanded="False"> 50 <section name="adv" title="Advanced Options" expanded="False">
57 <param argument="--evalue" type="float" value="0.01" label="E-value cutoff for BLAST searches."/> 51 <param argument="--evalue" type="float" value="0.01" label="E-value cutoff for BLAST searches."/>
58 <param argument="--limit" type="integer" value="3" label="How many candidate regions to consider"/> 52 <param argument="--limit" type="integer" value="3" label="How many candidate regions to consider"/>
67 <when value="history"> 61 <when value="history">
68 <param name="augustus_model" type="data" format="augustus" label="Augustus model"/> 62 <param name="augustus_model" type="data" format="augustus" label="Augustus model"/>
69 </when> 63 </when>
70 <when value="builtin"> 64 <when value="builtin">
71 <param name="augustus_species" type="select" label="Augustus species model"> 65 <param name="augustus_species" type="select" label="Augustus species model">
72 <!-- If you update this list, please also update it in maker and augustus tools (../maker/maker.xml and ../augustus/augustus.xml) --> 66 <expand macro="augustus_species"/>
73 <option value="human">Homo sapiens</option>
74 <option value="fly">Drosophila melanogaster</option>
75 <option value="arabidopsis">Arabidopsis thaliana</option>
76 <option value="brugia ">Brugia malayi</option>
77 <option value="aedes">Aedes aegypti</option>
78 <option value="tribolium2012">Tribolium castaneum</option>
79 <option value="schistosoma">Schistosoma mansoni</option>
80 <option value="tetrahymena">Tetrahymena thermophila</option>
81 <option value="galdieria">Galdieria sulphuraria</option>
82 <option value="maize">Zea mays</option>
83 <option value="toxoplasma">Toxoplasma gondii</option>
84 <option value="caenorhabditis ">Caenorhabditis elegans</option>
85 <option value="aspergillus_fumigatus">Aspergillus fumigatus</option>
86 <option value="aspergillus_nidulans ">Aspergillus nidulans</option>
87 <option value="aspergillus_oryzae ">Aspergillus oryzae</option>
88 <option value="aspergillus_terreus">Aspergillus terreus</option>
89 <option value="botrytis_cinerea ">Botrytis cinerea</option>
90 <option value="candida_albicans ">Candida albicans</option>
91 <option value="candida_guilliermondii ">Candida guilliermondii</option>
92 <option value="candida_tropicalis ">Candida tropicalis</option>
93 <option value="chaetomium_globosum">Chaetomium globosum</option>
94 <option value="coccidioides_immitis">Coccidioides immitis</option>
95 <option value="coprinus">Coprinus cinereus</option>
96 <option value="coprinus_cinereus">Coprinus cinereus</option>
97 <option value="cryptococcus_neoformans_gattii">Cryptococcus neoformans gattii</option>
98 <option value="cryptococcus_neoformans_neoformans_B">Cryptococcus neoformans neoformans</option>
99 <option value="cryptococcus_neoformans_neoformans_JEC21">Cryptococcus neoformans neoformans</option>
100 <option value="cryptococcus">Cryptococcus neoformans</option>
101 <option value="debaryomyces_hansenii">Debaryomyces hansenii</option>
102 <option value="encephalitozoon_cuniculi_GB">Encephalitozoon cuniculi</option>
103 <option value="eremothecium_gossypii">Eremothecium gossypii</option>
104 <option value="fusarium_graminearum ">Fusarium graminearum</option>
105 <option value="histoplasma_capsulatum ">Histoplasma capsulatum</option>
106 <option value="histoplasma">Histoplasma capsulatum</option>
107 <option value="kluyveromyces_lactis ">Kluyveromyces lactis</option>
108 <option value="laccaria_bicolor ">Laccaria bicolor</option>
109 <option value="lamprey">Petromyzon marinus</option>
110 <option value="leishmania_tarentolae">Leishmania tarentolae</option>
111 <option value="lodderomyces_elongisporus">Lodderomyces elongisporus</option>
112 <option value="magnaporthe_grisea ">Magnaporthe grisea</option>
113 <option value="neurospora_crassa">Neurospora crassa</option>
114 <option value="phanerochaete_chrysosporium">Phanerochaete chrysosporium</option>
115 <option value="pichia_stipitis">Pichia stipitis</option>
116 <option value="rhizopus_oryzae">Rhizopus oryzae</option>
117 <option value="saccharomyces_cerevisiae_S288C">Saccharomyces cerevisiae</option>
118 <option value="saccharomyces_cerevisiae_rm11-1a_1">Saccharomyces cerevisiae</option>
119 <option value="saccharomyces">Saccharomyces cerevisiae</option>
120 <option value="schizosaccharomyces_pombe">Schizosaccharomyces pombe</option>
121 <option value="trichinella">Trichinella spiralis</option>
122 <option value="ustilago_maydis">Ustilago maydis</option>
123 <option value="yarrowia_lipolytica">Yarrowia lipolytica</option>
124 <option value="nasonia">Nasonia vitripennis</option>
125 <option value="tomato">Solanum lycopersicum</option>
126 <option value="chlamydomonas">Chlamydomonas reinhardtii</option>
127 <option value="amphimedon">Amphimedon queenslandica</option>
128 <option value="pneumocystis">Pneumocystis jirovecii</option>
129 <option value="chicken">Gallus gallus domesticus (chicken)</option>
130 <option value="cacao">Theobroma cacao (cacao)</option>
131 <option value="heliconius_melpomene1">Heliconius melpomene</option>
132 <option value="xenoturbella">Xenoturbella</option>
133 <option value="E_coli_K12">E coli K12</option>
134 <option value="c_elegans_trsk">c elegans trsk</option>
135 <option value="camponotus_floridanus">Camponotus floridanus</option>
136 <option value="coyote_tobacco">Coyote tobacco</option>
137 <option value="s_aureus">Staphylococcus aureus</option>
138 <option value="thermoanaerobacter_tengcongensis">Thermoanaerobacter tengcongensis</option>
139 <option value="wheat">wheat</option>
140 <option value="zebrafish">Danio rerio</option>
141 <option value="anidulans">Aspergillus nidulans</option>
142 <option value="bombus_impatiens1">Bombus impatiens1</option>
143 <option value="bombus_terrestris2">Bombus terrestris2</option>
144 <option value="botrytis_cinerea">Botrytis cinerea</option>
145 <option value="brugia_malayi">Brugia malayi</option>
146 <option value="conidiobolus_coronatus">Conidiobolus coronatus</option>
147 <option value="cryptococcus_neoformans">Cryptococcus neoformans</option>
148 <option value="culex_pipiens">Culex pipiens</option>
149 <option value="elephant_shark">Callorhinchus milii</option>
150 <option value="honeybee1">Apis mellifera</option>
151 <option value="phanerochaete_chrysosporium">Phanerochaete chrysosporium</option>
152 <option value="pea_aphid">Acyrthosiphon pisum</option>
153 <option value="rhodnius_prolixus">Rhodnius prolixus</option>
154 <option value="ustilago_maydis">Ustilago maydis</option>
155 <option value="verticillium_albo_atrum1">Verticillium albo atrum1</option>
156 <option value="verticillium_longisporum1">Verticillium longisporum1</option>
157 <option value="Xipophorus_maculatus">Xipophorus_maculatus</option>
158 <option value="adorsata">adorsata</option>
159 <option value="ancylostoma_ceylanicum">ancylostoma_ceylanicum</option>
160 <option value="maker2_athal1">maker2_athal1</option>
161 <option value="maker2_c_elegans1">maker2_c_elegans1</option>
162 <option value="maker2_dmel1">maker2_dmel1</option>
163 <option value="maker2_spomb1">maker2_spomb1</option>
164 <option value="parasteatoda">parasteatoda</option>
165 <option value="rice">rice</option>
166 <option value="schistosoma2">schistosoma2</option>
167 <option value="sulfolobus_solfataricus">sulfolobus_solfataricus</option>
168 </param> 67 </param>
169 </when> 68 </when>
170 </conditional> 69 </conditional>
171 <param argument="--long" type="boolean" checked="false" truevalue="--long" falsevalue="" label="Optimization mode Augustus self-training" help="Adds considerably to run time, but can improve results for some non-model organisms"/> 70 <param argument="--long" type="boolean" checked="false" truevalue="--long" falsevalue="" label="Optimization mode Augustus self-training" help="Adds considerably to run time, but can improve results for some non-model organisms"/>
172 </section> 71 </section>
173 </inputs> 72 </inputs>
174 <outputs> 73 <outputs>
175 <data name='busco_sum' format='txt' label="${tool.name} on ${on_string}: short summary" from_work_dir="run_busco_galaxy/short_summary_busco_galaxy.txt"/> 74 <data name='busco_sum' format='txt' label="${tool.name} on ${on_string}: short summary" from_work_dir="busco_galaxy/run_*/short_summary.txt"/>
176 <data name='busco_table' format='tabular' label="${tool.name} on ${on_string}: full table" from_work_dir="run_busco_galaxy/full_table_busco_galaxy.tsv"/> 75 <data name='busco_table' format='tabular' label="${tool.name} on ${on_string}: full table" from_work_dir="busco_galaxy/run_*/full_table.tsv"/>
177 <data name='busco_missing' format='tabular' label="${tool.name} on ${on_string}: missing buscos" from_work_dir="run_busco_galaxy/missing_busco_list_busco_galaxy.tsv"/> 76 <data name='busco_missing' format='tabular' label="${tool.name} on ${on_string}: missing buscos" from_work_dir="busco_galaxy/run_*/missing_busco_list.tsv"/>
178 </outputs> 77 </outputs>
179 <tests> 78 <tests>
180 <test> 79 <test>
181 <param name="input" value="genome.fa"/> 80 <param name="input" value="genome.fa"/>
182 <param name="lineage_path" value="arthropoda"/> 81 <param name="lineage_dataset" value="arthropoda_odb10"/>
183 <param name="mode" value="geno"/> 82 <param name="mode" value="geno"/>
184 <output name="busco_sum" file="genome_results/short_summary" compare="diff" lines_diff="4"/> 83 <output name="busco_sum" file="genome_results/short_summary" compare="diff" lines_diff="4"/>
185 <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="4"/> 84 <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="4"/>
186 <output name="busco_missing" file="genome_results/missing_buscos_list" compare="diff" lines_diff="4"/> 85 <output name="busco_missing" file="genome_results/missing_buscos_list" compare="diff" lines_diff="4"/>
187 </test> 86 </test>
188 <test> 87 <test>
189 <param name="input" value="proteome.fa"/> 88 <param name="input" value="proteome.fa"/>
190 <param name="lineage_path" value="arthropoda"/> 89 <param name="lineage_dataset" value="arthropoda_odb10"/>
191 <param name="mode" value="prot"/> 90 <param name="mode" value="prot"/>
192 <output name="busco_sum" file="proteome_results/short_summary" compare="diff" lines_diff="4"/> 91 <output name="busco_sum" file="proteome_results/short_summary" compare="diff" lines_diff="4"/>
193 <output name="busco_table" file="proteome_results/full_table" compare="diff" lines_diff="4"/> 92 <output name="busco_table" file="proteome_results/full_table" compare="diff" lines_diff="4"/>
194 <output name="busco_missing" file="proteome_results/missing_buscos_list" compare="diff" lines_diff="4"/> 93 <output name="busco_missing" file="proteome_results/missing_buscos_list" compare="diff" lines_diff="4"/>
195 </test> 94 </test>
196 <test> 95 <test>
197 <param name="input" value="transcriptome.fa"/> 96 <param name="input" value="transcriptome.fa"/>
198 <param name="lineage_path" value="arthropoda"/> 97 <param name="lineage_dataset" value="arthropoda_odb10"/>
199 <param name="mode" value="tran"/> 98 <param name="mode" value="tran"/>
200 <output name="busco_sum" file="transcriptome_results/short_summary" compare="diff" lines_diff="4"/> 99 <output name="busco_sum" file="transcriptome_results/short_summary" compare="diff" lines_diff="4"/>
201 <output name="busco_table" file="transcriptome_results/full_table" compare="diff" lines_diff="4"/> 100 <output name="busco_table" file="transcriptome_results/full_table" compare="diff" lines_diff="4"/>
202 <output name="busco_missing" file="transcriptome_results/missing_buscos_list" compare="diff" lines_diff="4"/> 101 <output name="busco_missing" file="transcriptome_results/missing_buscos_list" compare="diff" lines_diff="4"/>
203 </test> 102 </test>
204 <test> 103 <test>
205 <param name="input" value="genome.fa"/> 104 <param name="input" value="genome.fa"/>
206 <param name="lineage_path" value="arthropoda"/> 105 <param name="lineage_dataset" value="arthropoda_odb10"/>
207 <param name="mode" value="geno"/> 106 <param name="mode" value="geno"/>
208 <param name="adv|aug_prediction|augustus_mode" value="builtin"/> 107 <param name="adv|aug_prediction|augustus_mode" value="builtin"/>
209 <param name="adv|aug_prediction|augustus_species" value="human"/> 108 <param name="adv|aug_prediction|augustus_species" value="human"/>
210 <output name="busco_sum" file="genome_results/short_summary" compare="diff" lines_diff="4"/> 109 <output name="busco_sum" file="genome_results/short_summary" compare="diff" lines_diff="4"/>
211 <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="4"/> 110 <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="4"/>
212 <output name="busco_missing" file="genome_results/missing_buscos_list" compare="diff" lines_diff="4"/> 111 <output name="busco_missing" file="genome_results/missing_buscos_list" compare="diff" lines_diff="4"/>
213 </test> 112 </test>
214 <test> 113 <test>
215 <param name="input" value="genome.fa"/> 114 <param name="input" value="genome.fa"/>
216 <param name="lineage_path" value="arthropoda"/> 115 <param name="lineage_dataset" value="arthropoda_odb10"/>
217 <param name="mode" value="geno"/> 116 <param name="mode" value="geno"/>
218 <param name="adv|aug_prediction|augustus_mode" value="history"/> 117 <param name="adv|aug_prediction|augustus_mode" value="history"/>
219 <param name="adv|aug_prediction|augustus_model" value="local.tar.gz" ftype="augustus"/> 118 <param name="adv|aug_prediction|augustus_model" value="local.tar.gz" ftype="augustus"/>
220 <output name="busco_sum" file="genome_results/short_summary" compare="diff" lines_diff="4"/> 119 <output name="busco_sum" file="genome_results/short_summary" compare="diff" lines_diff="4"/>
221 <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="4"/> 120 <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="4"/>
225 <help> 124 <help>
226 BUSCO: assessing genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs 125 BUSCO: assessing genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs
227 126
228 .. _BUSCO: http://busco.ezlab.org/ 127 .. _BUSCO: http://busco.ezlab.org/
229 </help> 128 </help>
230 <citations> 129 <expand macro="citations"/>
231 <citation type="doi">doi:10.1093/bioinformatics/btv351</citation>
232 </citations>
233 </tool> 130 </tool>