comparison maker.xml @ 2:d3a2072d8745 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 4141a68e0ce1cf6a24f721dce31b81b56f249088

1:73a79dec987b

<?xml version="1.0"?>
<tool id="maker" name="Maker" profile="16.04" version="@VERSION@.1">
    <description>genome annotation pipeline</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>

        maker -CTL

        &&

        sed "s/cpus=/cpus=\${GALAXY_SLOTS:-4}/g" '$ctl' > maker_opts.ctl

        &&

        #if $abinitio_gene_prediction.aug_prediction.augustus_mode == 'history'

            tar -C 'augustus_dir/species/' -xzvf '${abinitio_gene_prediction.aug_prediction.augustus_model}' > /dev/null &&

            export AUGUSTUS_CONFIG_PATH=`pwd`/augustus_dir/ &&
        #end if

        maker maker_opts.ctl maker_bopts.ctl maker_exe.ctl

        &&

        gff3_merge -d *.maker.output/*_master_datastore_index.log -o '${output_full}'

other_gff= # extra features to pass-through to final MAKER generated GFF3 file
#end if

#-----External Application Behavior Options
alt_peptide=${advanced.alt_peptide} # amino acid used to replace non-standard amino acids in BLAST databases
cpus= # max number of cpus to use in BLAST and RepeatMasker (not for MPI, leave 1 when using MPI)

#-----MAKER Behavior Options
max_dna_len=${advanced.max_dna_len} # length for dividing up contigs into chunks (increases/decreases memory usage)
min_contig=${advanced.min_contig} # skip genome contigs below this length (under 10kb are often useless)

2:d3a2072d8745

<?xml version="1.0"?>
<tool id="maker" name="Maker" profile="16.04" version="@VERSION@">
    <description>genome annotation pipeline</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>

        maker -CTL

        &&

        cp '$ctl' maker_opts.ctl

        &&

        #if $abinitio_gene_prediction.aug_prediction.augustus_mode == 'history'

            tar -C 'augustus_dir/species/' -xzvf '${abinitio_gene_prediction.aug_prediction.augustus_model}' > /dev/null &&

            export AUGUSTUS_CONFIG_PATH=`pwd`/augustus_dir/ &&
        #end if

        mpiexec -n \${GALAXY_SLOTS:-4} maker maker_opts.ctl maker_bopts.ctl maker_exe.ctl < /dev/null

        &&

        gff3_merge -d *.maker.output/*_master_datastore_index.log -o '${output_full}'

other_gff= # extra features to pass-through to final MAKER generated GFF3 file
#end if

#-----External Application Behavior Options
alt_peptide=${advanced.alt_peptide} # amino acid used to replace non-standard amino acids in BLAST databases
cpus=1 # max number of cpus to use in BLAST and RepeatMasker (not for MPI, leave 1 when using MPI)

#-----MAKER Behavior Options
max_dna_len=${advanced.max_dna_len} # length for dividing up contigs into chunks (increases/decreases memory usage)
min_contig=${advanced.min_contig} # skip genome contigs below this length (under 10kb are often useless)