Mercurial > repos > greg > phylogenomics_analysis

comparison phylogenomics_analysis.xml @ 38:5423ad5c4f00 draft

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author greg
date Tue, 24 Jan 2017 10:33:16 -0500
parents 79c8d886e43b
children 53f404994667
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37:79c8d886e43b 38:5423ad5c4f00
53 53
54 mkdir -p $dest_fasta_dir && 54 mkdir -p $dest_fasta_dir &&
55 55
56 PhylogenomicsAnalysis 56 PhylogenomicsAnalysis
57 --num_threads \${GALAXY_SLOTS:-4} 57 --num_threads \${GALAXY_SLOTS:-4}
58 --no_config_override
59 --orthogroup_faa "$orthogroup_faa.extra_files_path" 58 --orthogroup_faa "$orthogroup_faa.extra_files_path"
60 --scaffold_dir "${GALAXY_DATA_INDEX_DIR}/plant_tribes/scaffolds" 59 --scaffold_dir "${GALAXY_DATA_INDEX_DIR}/plant_tribes/scaffolds"
61 --scaffold "$scaffold" 60 --scaffold "$scaffold"
62 --method $method 61 --method $method
63 62