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comparison maker.xml @ 2:be967733bf81 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 4141a68e0ce1cf6a24f721dce31b81b56f249088
author iuc
date Fri, 03 May 2019 07:49:50 -0400
parents c98b3fa910bf
children 681e5067048e
comparison
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1:c98b3fa910bf 2:be967733bf81
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="maker" name="Maker" profile="16.04" version="@VERSION@.1"> 2 <tool id="maker" name="Maker" profile="16.04" version="@VERSION@">
3 <description>genome annotation pipeline</description> 3 <description>genome annotation pipeline</description>
4 <macros> 4 <macros>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
7 <expand macro="requirements"/> 7 <expand macro="requirements"/>
16 16
17 maker -CTL 17 maker -CTL
18 18
19 && 19 &&
20 20
21 sed "s/cpus=/cpus=\${GALAXY_SLOTS:-4}/g" '$ctl' > maker_opts.ctl 21 cp '$ctl' maker_opts.ctl
22 22
23 && 23 &&
24 24
25 #if $abinitio_gene_prediction.aug_prediction.augustus_mode == 'history' 25 #if $abinitio_gene_prediction.aug_prediction.augustus_mode == 'history'
26 26
33 tar -C 'augustus_dir/species/' -xzvf '${abinitio_gene_prediction.aug_prediction.augustus_model}' > /dev/null && 33 tar -C 'augustus_dir/species/' -xzvf '${abinitio_gene_prediction.aug_prediction.augustus_model}' > /dev/null &&
34 34
35 export AUGUSTUS_CONFIG_PATH=`pwd`/augustus_dir/ && 35 export AUGUSTUS_CONFIG_PATH=`pwd`/augustus_dir/ &&
36 #end if 36 #end if
37 37
38 maker maker_opts.ctl maker_bopts.ctl maker_exe.ctl 38 mpiexec -n \${GALAXY_SLOTS:-4} maker maker_opts.ctl maker_bopts.ctl maker_exe.ctl < /dev/null
39 39
40 && 40 &&
41 41
42 gff3_merge -d *.maker.output/*_master_datastore_index.log -o '${output_full}' 42 gff3_merge -d *.maker.output/*_master_datastore_index.log -o '${output_full}'
43 43
190 other_gff= # extra features to pass-through to final MAKER generated GFF3 file 190 other_gff= # extra features to pass-through to final MAKER generated GFF3 file
191 #end if 191 #end if
192 192
193 #-----External Application Behavior Options 193 #-----External Application Behavior Options
194 alt_peptide=${advanced.alt_peptide} # amino acid used to replace non-standard amino acids in BLAST databases 194 alt_peptide=${advanced.alt_peptide} # amino acid used to replace non-standard amino acids in BLAST databases
195 cpus= # max number of cpus to use in BLAST and RepeatMasker (not for MPI, leave 1 when using MPI) 195 cpus=1 # max number of cpus to use in BLAST and RepeatMasker (not for MPI, leave 1 when using MPI)
196 196
197 #-----MAKER Behavior Options 197 #-----MAKER Behavior Options
198 max_dna_len=${advanced.max_dna_len} # length for dividing up contigs into chunks (increases/decreases memory usage) 198 max_dna_len=${advanced.max_dna_len} # length for dividing up contigs into chunks (increases/decreases memory usage)
199 min_contig=${advanced.min_contig} # skip genome contigs below this length (under 10kb are often useless) 199 min_contig=${advanced.min_contig} # skip genome contigs below this length (under 10kb are often useless)
200 200