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comparison busco.xml @ 2:d010a90f588e draft

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planemo upload commit 99b8e51a68074a214ca4415a635a426e80e4129b
author iuc
date Fri, 14 Dec 2018 08:12:42 -0500
parents 0b9b7d845c2a
children fe39db248196
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1:0b9b7d845c2a 2:d010a90f588e
1 <tool id="busco" name="Busco" version="2.0"> 1 <tool id="busco" name="Busco" version="3.0.2">
2 <description>assess genome assembly and annotation completeness</description> 2 <description>assess genome assembly and annotation completeness</description>
3
4 <requirements> 3 <requirements>
5 <requirement type="package" version="2.0">busco</requirement> 4 <requirement type="package" version="3.0.2">busco</requirement>
5 <requirement type="package" version="2.2.1">r-ggplot2</requirement>
6 </requirements> 6 </requirements>
7
8 <command><![CDATA[ 7 <command><![CDATA[
9 BUSCO.py 8 export BUSCO_CONFIG_FILE='busco_config.ini'
9
10 &&
11
12 if [ -z "\$AUGUSTUS_CONFIG_PATH" ] ; then BUSCO_PATH=\$(dirname \$(which run_BUSCO.py)) ; export AUGUSTUS_CONFIG_PATH=\$(realpath \${BUSCO_PATH}/../config) ; fi &&
13 cp -r "\$AUGUSTUS_CONFIG_PATH/" augustus_dir/ &&
14 export AUGUSTUS_CONFIG_PATH=`pwd`/augustus_dir/ &&
15
16 #if $adv.aug_prediction.augustus_mode == 'history':
17 ## Using an augustus model from history, we need to unzip it and let augustus find it
18
19 mkdir -p 'augustus_dir/species/' &&
20
21 tar -C 'augustus_dir/species/' -xzvf '${adv.aug_prediction.augustus_model}' > /dev/null &&
22 #end if
23
24 run_BUSCO.py
10 --in '${input}' 25 --in '${input}'
11 --lineage '${lineage.fields.path}' 26 --lineage_path '${lineage_path.fields.path}/${lineage_path.fields.value}'
12 --mode '${mode}' 27 --mode '${mode}'
13 -o "busco_galaxy" 28 -o "busco_galaxy"
14 --cpu \${GALAXY_SLOTS:-4} 29 --cpu \${GALAXY_SLOTS:-4}
15 --evalue ${adv.evalue} 30 --evalue ${adv.evalue}
16 ${adv.long} 31 ${adv.long}
17 --limit ${adv.limit} 32 --limit ${adv.limit}
18 #if $adv.species: 33 #if $adv.aug_prediction.augustus_mode == 'builtin':
19 --species '${adv.species}' 34 --species '${adv.aug_prediction.augustus_species}'
35 #else if $adv.aug_prediction.augustus_mode == 'history':
36 --species local
20 #end if 37 #end if
21 --tarzip 38 --tarzip
22 ]]></command> 39 ]]></command>
23 40
24 <inputs> 41 <inputs>
25 42
26 <param type="data" name="input" format="fasta" label="Sequences to analyse" help="genome, transcriptome or proteome" /> 43 <param type="data" name="input" format="fasta" label="Sequences to analyse" help="genome, transcriptome or proteome" />
27
28 <param argument="--mode" type="select" label="Mode"> 44 <param argument="--mode" type="select" label="Mode">
29 <option value="geno">Genome</option> 45 <option value="geno">Genome</option>
30 <option value="tran">Transcriptome</option> 46 <option value="tran">Transcriptome</option>
31 <option value="prot">Proteome</option> 47 <option value="prot">Proteome</option>
32 </param> 48 </param>
33 49
34 <param argument="--lineage" type="select" label="Lineage"> 50 <param argument="--lineage_path" type="select" label="Lineage">
35 <options from_data_table="busco"> 51 <options from_data_table="busco">
36 <filter type="sort_by" column="2" /> 52 <filter type="sort_by" column="2" />
37 <validator type="no_options" message="No indexes are available" /> 53 <validator type="no_options" message="No indexes are available" />
38 </options> 54 </options>
39 </param> 55 </param>
40 56
41 <section name="adv" title="Advanced Options" expanded="False"> 57 <section name="adv" title="Advanced Options" expanded="False">
42 <param argument="--evalue" type="float" value="0.01" label="E-value cutoff for BLAST searches."/> 58 <param argument="--evalue" type="float" value="0.01" label="E-value cutoff for BLAST searches."/>
43 <param argument="--limit" type="integer" value="3" label="How many candidate regions to consider"/> 59 <param argument="--limit" type="integer" value="3" label="How many candidate regions to consider"/>
44 <param argument="--species" type="text" optional="True" label="Name of existing Augustus species gene finding metaparameters"/> 60
61 <conditional name="aug_prediction">
62 <param name="augustus_mode" type="select" label="Augustus species model">
63 <option value="no" selected="true">Use the default species for selected lineage</option>
64 <option value="builtin">Use another predefined species model</option>
65 <option value="history">Use a custom species model</option>
66 </param>
67 <when value="no"/>
68 <when value="history">
69 <param name="augustus_model" type="data" format="augustus" label="Augustus model"/>
70 </when>
71 <when value="builtin">
72 <param name="augustus_species" type="select" label="Augustus species model">
73 <!-- If you update this list, please also update it in maker and augustus tools (../maker/maker.xml and ../augustus/augustus.xml) -->
74 <option value="human">Homo sapiens</option>
75 <option value="fly">Drosophila melanogaster</option>
76 <option value="arabidopsis">Arabidopsis thaliana</option>
77 <option value="brugia ">Brugia malayi</option>
78 <option value="aedes">Aedes aegypti</option>
79 <option value="tribolium2012">Tribolium castaneum</option>
80 <option value="schistosoma">Schistosoma mansoni</option>
81 <option value="tetrahymena">Tetrahymena thermophila</option>
82 <option value="galdieria">Galdieria sulphuraria</option>
83 <option value="maize">Zea mays</option>
84 <option value="toxoplasma">Toxoplasma gondii</option>
85 <option value="caenorhabditis ">Caenorhabditis elegans</option>
86 <option value="aspergillus_fumigatus">Aspergillus fumigatus</option>
87 <option value="aspergillus_nidulans ">Aspergillus nidulans</option>
88 <option value="aspergillus_oryzae ">Aspergillus oryzae</option>
89 <option value="aspergillus_terreus">Aspergillus terreus</option>
90 <option value="botrytis_cinerea ">Botrytis cinerea</option>
91 <option value="candida_albicans ">Candida albicans</option>
92 <option value="candida_guilliermondii ">Candida guilliermondii</option>
93 <option value="candida_tropicalis ">Candida tropicalis</option>
94 <option value="chaetomium_globosum">Chaetomium globosum</option>
95 <option value="coccidioides_immitis">Coccidioides immitis</option>
96 <option value="coprinus">Coprinus cinereus</option>
97 <option value="coprinus_cinereus">Coprinus cinereus</option>
98 <option value="cryptococcus_neoformans_gattii">Cryptococcus neoformans gattii</option>
99 <option value="cryptococcus_neoformans_neoformans_B">Cryptococcus neoformans neoformans</option>
100 <option value="cryptococcus_neoformans_neoformans_JEC21">Cryptococcus neoformans neoformans</option>
101 <option value="cryptococcus">Cryptococcus neoformans</option>
102 <option value="debaryomyces_hansenii">Debaryomyces hansenii</option>
103 <option value="encephalitozoon_cuniculi_GB">Encephalitozoon cuniculi</option>
104 <option value="eremothecium_gossypii">Eremothecium gossypii</option>
105 <option value="fusarium_graminearum ">Fusarium graminearum</option>
106 <option value="histoplasma_capsulatum ">Histoplasma capsulatum</option>
107 <option value="histoplasma">Histoplasma capsulatum</option>
108 <option value="kluyveromyces_lactis ">Kluyveromyces lactis</option>
109 <option value="laccaria_bicolor ">Laccaria bicolor</option>
110 <option value="lamprey">Petromyzon marinus</option>
111 <option value="leishmania_tarentolae">Leishmania tarentolae</option>
112 <option value="lodderomyces_elongisporus">Lodderomyces elongisporus</option>
113 <option value="magnaporthe_grisea ">Magnaporthe grisea</option>
114 <option value="neurospora_crassa">Neurospora crassa</option>
115 <option value="phanerochaete_chrysosporium">Phanerochaete chrysosporium</option>
116 <option value="pichia_stipitis">Pichia stipitis</option>
117 <option value="rhizopus_oryzae">Rhizopus oryzae</option>
118 <option value="saccharomyces_cerevisiae_S288C">Saccharomyces cerevisiae</option>
119 <option value="saccharomyces_cerevisiae_rm11-1a_1">Saccharomyces cerevisiae</option>
120 <option value="saccharomyces">Saccharomyces cerevisiae</option>
121 <option value="schizosaccharomyces_pombe">Schizosaccharomyces pombe</option>
122 <option value="trichinella">Trichinella spiralis</option>
123 <option value="ustilago_maydis">Ustilago maydis</option>
124 <option value="yarrowia_lipolytica">Yarrowia lipolytica</option>
125 <option value="nasonia">Nasonia vitripennis</option>
126 <option value="tomato">Solanum lycopersicum</option>
127 <option value="chlamydomonas">Chlamydomonas reinhardtii</option>
128 <option value="amphimedon">Amphimedon queenslandica</option>
129 <option value="pneumocystis">Pneumocystis jirovecii</option>
130 <option value="chicken">Gallus gallus domesticus (chicken)</option>
131 <option value="cacao">Theobroma cacao (cacao)</option>
132 <option value="heliconius_melpomene1">Heliconius melpomene</option>
133 <option value="xenoturbella">Xenoturbella</option>
134 <option value="E_coli_K12">E coli K12</option>
135 <option value="c_elegans_trsk">c elegans trsk</option>
136 <option value="camponotus_floridanus">Camponotus floridanus</option>
137 <option value="coyote_tobacco">Coyote tobacco</option>
138 <option value="s_aureus">Staphylococcus aureus</option>
139 <option value="thermoanaerobacter_tengcongensis">Thermoanaerobacter tengcongensis</option>
140 <option value="wheat">wheat</option>
141 <option value="zebrafish">Danio rerio</option>
142 <option value="anidulans">Aspergillus nidulans</option>
143 <option value="bombus_impatiens1">Bombus impatiens1</option>
144 <option value="bombus_terrestris2">Bombus terrestris2</option>
145 <option value="botrytis_cinerea">Botrytis cinerea</option>
146 <option value="brugia_malayi">Brugia malayi</option>
147 <option value="conidiobolus_coronatus">Conidiobolus coronatus</option>
148 <option value="cryptococcus_neoformans">Cryptococcus neoformans</option>
149 <option value="culex_pipiens">Culex pipiens</option>
150 <option value="elephant_shark">Callorhinchus milii</option>
151 <option value="honeybee1">Apis mellifera</option>
152 <option value="phanerochaete_chrysosporium">Phanerochaete chrysosporium</option>
153 <option value="pea_aphid">Acyrthosiphon pisum</option>
154 <option value="rhodnius_prolixus">Rhodnius prolixus</option>
155 <option value="ustilago_maydis">Ustilago maydis</option>
156 <option value="verticillium_albo_atrum1">Verticillium albo atrum1</option>
157 <option value="verticillium_longisporum1">Verticillium longisporum1</option>
158 <option value="Xipophorus_maculatus">Xipophorus_maculatus</option>
159 <option value="adorsata">adorsata</option>
160 <option value="ancylostoma_ceylanicum">ancylostoma_ceylanicum</option>
161 <option value="maker2_athal1">maker2_athal1</option>
162 <option value="maker2_c_elegans1">maker2_c_elegans1</option>
163 <option value="maker2_dmel1">maker2_dmel1</option>
164 <option value="maker2_spomb1">maker2_spomb1</option>
165 <option value="parasteatoda">parasteatoda</option>
166 <option value="rice">rice</option>
167 <option value="schistosoma2">schistosoma2</option>
168 <option value="sulfolobus_solfataricus">sulfolobus_solfataricus</option>
169 </param>
170 </when>
171 </conditional>
45 <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 <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"/>
46 </section> 173 </section>
47 </inputs> 174 </inputs>
48 <outputs> 175 <outputs>
49 <data name='busco_sum' format='txt' label="${tool.name} on ${on_string}: short summary" from_work_dir="run_busco_galaxy/short_summary_busco_galaxy.txt"/> 176 <data name='busco_sum' format='txt' label="${tool.name} on ${on_string}: short summary" from_work_dir="run_busco_galaxy/short_summary_busco_galaxy.txt"/>
51 <data name='busco_missing' format='tabular' label="${tool.name} on ${on_string}: missing buscos" from_work_dir="run_busco_galaxy/missing_busco_list_busco_galaxy.tsv"/> 178 <data name='busco_missing' format='tabular' label="${tool.name} on ${on_string}: missing buscos" from_work_dir="run_busco_galaxy/missing_busco_list_busco_galaxy.tsv"/>
52 </outputs> 179 </outputs>
53 <tests> 180 <tests>
54 <test> 181 <test>
55 <param name="input" value="genome.fa"/> 182 <param name="input" value="genome.fa"/>
56 <param name="lineage" value="arthropoda_2.0"/> 183 <param name="lineage_path" value="arthropoda"/>
57 <param name="mode" value="geno"/> 184 <param name="mode" value="geno"/>
58 <output name="busco_sum" file="genome_results/short_summary" compare="diff" lines_diff="4"/> 185 <output name="busco_sum" file="genome_results/short_summary" compare="diff" lines_diff="4"/>
59 <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="4"/> 186 <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="4"/>
60 <output name="busco_missing" file="genome_results/missing_buscos_list" compare="diff" lines_diff="4"/> 187 <output name="busco_missing" file="genome_results/missing_buscos_list" compare="diff" lines_diff="4"/>
61 </test> 188 </test>
62 <test> 189 <test>
63 <param name="input" value="proteome.fa"/> 190 <param name="input" value="proteome.fa"/>
64 <param name="lineage" value="arthropoda_2.0"/> 191 <param name="lineage_path" value="arthropoda"/>
65 <param name="mode" value="prot"/> 192 <param name="mode" value="prot"/>
66 <output name="busco_sum" file="proteome_results/short_summary" compare="diff" lines_diff="4"/> 193 <output name="busco_sum" file="proteome_results/short_summary" compare="diff" lines_diff="4"/>
67 <output name="busco_table" file="proteome_results/full_table" compare="diff" lines_diff="4"/> 194 <output name="busco_table" file="proteome_results/full_table" compare="diff" lines_diff="4"/>
68 <output name="busco_missing" file="proteome_results/missing_buscos_list" compare="diff" lines_diff="4"/> 195 <output name="busco_missing" file="proteome_results/missing_buscos_list" compare="diff" lines_diff="4"/>
69 </test> 196 </test>
70 <test> 197 <test>
71 <param name="input" value="transcriptome.fa"/> 198 <param name="input" value="transcriptome.fa"/>
72 <param name="lineage" value="arthropoda_2.0"/> 199 <param name="lineage_path" value="arthropoda"/>
73 <param name="mode" value="tran"/> 200 <param name="mode" value="tran"/>
74 <output name="busco_sum" file="transcriptome_results/short_summary" compare="diff" lines_diff="4"/> 201 <output name="busco_sum" file="transcriptome_results/short_summary" compare="diff" lines_diff="4"/>
75 <output name="busco_table" file="transcriptome_results/full_table" compare="diff" lines_diff="4"/> 202 <output name="busco_table" file="transcriptome_results/full_table" compare="diff" lines_diff="4"/>
76 <output name="busco_missing" file="transcriptome_results/missing_buscos_list" compare="diff" lines_diff="4"/> 203 <output name="busco_missing" file="transcriptome_results/missing_buscos_list" compare="diff" lines_diff="4"/>
77 </test> 204 </test>
205 <test>
206 <param name="input" value="genome.fa"/>
207 <param name="lineage_path" value="arthropoda"/>
208 <param name="mode" value="geno"/>
209 <param name="adv|aug_prediction|augustus_mode" value="builtin"/>
210 <param name="adv|aug_prediction|augustus_species" value="human"/>
211 <output name="busco_sum" file="genome_results/short_summary" compare="diff" lines_diff="4"/>
212 <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="4"/>
213 <output name="busco_missing" file="genome_results/missing_buscos_list" compare="diff" lines_diff="4"/>
214 </test>
215 <test>
216 <param name="input" value="genome.fa"/>
217 <param name="lineage_path" value="arthropoda"/>
218 <param name="mode" value="geno"/>
219 <param name="adv|aug_prediction|augustus_mode" value="history"/>
220 <param name="adv|aug_prediction|augustus_model" value="local.tar.gz" ftype="augustus"/>
221 <output name="busco_sum" file="genome_results/short_summary" compare="diff" lines_diff="4"/>
222 <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="4"/>
223 <output name="busco_missing" file="genome_results/missing_buscos_list" compare="diff" lines_diff="4"/>
224 </test>
78 </tests> 225 </tests>
79 <help> 226 <help>
80 BUSCO: assessing genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs 227 BUSCO: assessing genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs
81 228
82 .. _BUSCO: http://busco.ezlab.org/ 229 .. _BUSCO: http://busco.ezlab.org/