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comparison busco.xml @ 4:5ecdeca79a0d draft

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planemo upload commit a91c8bf878080b84ef938e1f95217c6bf3f0cba1
author iuc
date Thu, 21 Feb 2019 14:33:28 -0500
parents f18f0b887c31
children 1440ae06552f
comparison
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3:f18f0b887c31 4:5ecdeca79a0d
1 <tool id="busco" name="Busco" version="3.0.2"> 1 <tool id="busco" name="Busco" version="@TOOL_VERSION@+galaxy0">
2 <description>assess genome assembly and annotation completeness</description> 2 <description>assess genome assembly and annotation completeness</description>
3 <macros>
4 <token name="@TOOL_VERSION@">3.0.2</token>
5 </macros>
3 <requirements> 6 <requirements>
4 <requirement type="package" version="3.0.2">busco</requirement> 7 <requirement type="package" version="@TOOL_VERSION@">busco</requirement>
5 <requirement type="package" version="2.2.1">r-ggplot2</requirement> 8 <requirement type="package" version="3.5.1">r-base</requirement>
6 </requirements> 9 </requirements>
7 <command><![CDATA[ 10 <command><![CDATA[
8 export BUSCO_CONFIG_FILE='busco_config.ini' 11 export BUSCO_CONFIG_FILE='busco_config.ini' &&
9 12 if [ -z "\$AUGUSTUS_CONFIG_PATH" ] ; then BUSCO_PATH=\$(dirname \$(which run_BUSCO.py)) ; export AUGUSTUS_CONFIG_PATH=\$(realpath \${BUSCO_PATH}/../config) ; fi &&
10 && 13 cp -r "\$AUGUSTUS_CONFIG_PATH/" augustus_dir/ &&
11 14 export AUGUSTUS_CONFIG_PATH=`pwd`/augustus_dir/ &&
12 if [ -z "\$AUGUSTUS_CONFIG_PATH" ] ; then BUSCO_PATH=\$(dirname \$(which run_BUSCO.py)) ; export AUGUSTUS_CONFIG_PATH=\$(realpath \${BUSCO_PATH}/../config) ; fi && 15
13 cp -r "\$AUGUSTUS_CONFIG_PATH/" augustus_dir/ && 16 #if $adv.aug_prediction.augustus_mode == 'history':
14 export AUGUSTUS_CONFIG_PATH=`pwd`/augustus_dir/ && 17 ## Using an augustus model from history, we need to unzip it and let augustus find it
15 18 mkdir -p 'augustus_dir/species/' &&
16 #if $adv.aug_prediction.augustus_mode == 'history': 19 tar -C 'augustus_dir/species/' -xzvf '${adv.aug_prediction.augustus_model}' > /dev/null &&
17 ## Using an augustus model from history, we need to unzip it and let augustus find it 20 #end if
18 21
19 mkdir -p 'augustus_dir/species/' && 22 run_BUSCO.py
20 23 --in '${input}'
21 tar -C 'augustus_dir/species/' -xzvf '${adv.aug_prediction.augustus_model}' > /dev/null && 24 --lineage_path '${lineage_path.fields.path}/${lineage_path.fields.value}'
22 #end if 25 --mode '${mode}'
23 26 -o busco_galaxy
24 run_BUSCO.py 27 --cpu \${GALAXY_SLOTS:-4}
25 --in '${input}' 28 --evalue ${adv.evalue}
26 --lineage_path '${lineage_path.fields.path}/${lineage_path.fields.value}' 29 ${adv.long}
27 --mode '${mode}' 30 --limit ${adv.limit}
28 -o "busco_galaxy" 31 #if $adv.aug_prediction.augustus_mode == 'builtin':
29 --cpu \${GALAXY_SLOTS:-4} 32 --species '${adv.aug_prediction.augustus_species}'
30 --evalue ${adv.evalue} 33 #else if $adv.aug_prediction.augustus_mode == 'history':
31 ${adv.long} 34 --species local
32 --limit ${adv.limit} 35 #end if
33 #if $adv.aug_prediction.augustus_mode == 'builtin': 36 --tarzip
34 --species '${adv.aug_prediction.augustus_species}'
35 #else if $adv.aug_prediction.augustus_mode == 'history':
36 --species local
37 #end if
38 --tarzip
39 ]]></command> 37 ]]></command>
40 38
41 <inputs> 39 <inputs>
42
43 <param type="data" name="input" format="fasta" label="Sequences to analyse" help="genome, transcriptome or proteome" /> 40 <param type="data" name="input" format="fasta" label="Sequences to analyse" help="genome, transcriptome or proteome" />
44 <param argument="--mode" type="select" label="Mode"> 41 <param argument="--mode" type="select" label="Mode">
45 <option value="geno">Genome</option> 42 <option value="geno">Genome</option>
46 <option value="tran">Transcriptome</option> 43 <option value="tran">Transcriptome</option>
47 <option value="prot">Proteome</option> 44 <option value="prot">Proteome</option>
222 <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="4"/> 219 <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"/> 220 <output name="busco_missing" file="genome_results/missing_buscos_list" compare="diff" lines_diff="4"/>
224 </test> 221 </test>
225 </tests> 222 </tests>
226 <help> 223 <help>
227 BUSCO: assessing genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs 224 BUSCO: assessing genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs
228 225
229 .. _BUSCO: http://busco.ezlab.org/ 226 .. _BUSCO: http://busco.ezlab.org/
230 </help> 227 </help>
231
232 <citations> 228 <citations>
233 <citation type="doi">doi:10.1093/bioinformatics/btv351</citation> 229 <citation type="doi">doi:10.1093/bioinformatics/btv351</citation>
234 </citations> 230 </citations>
235 </tool> 231 </tool>