Mercurial > repos > greg > phylogenomics_analysis

comparison phylogenomics_analysis.xml @ 32:c2ec4bb1fd5f draft

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author greg
date Wed, 11 Jan 2017 13:32:18 -0500
parents 40a1cb4c8426
children d8e7ac110e1b
comparison
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31:40a1cb4c8426 32:c2ec4bb1fd5f
52 #end if 52 #end if
53 53
54 mkdir -p $dest_fasta_dir && 54 mkdir -p $dest_fasta_dir &&
55 55
56 PhylogenomicsAnalysis 56 PhylogenomicsAnalysis
57 --num_threads "\${GALAXY_SLOTS:-4}" 57 --num_threads \${GALAXY_SLOTS:-4}
58 --no_config_override
58 --orthogroup_faa "$orthogroup_faa.extra_files_path" 59 --orthogroup_faa "$orthogroup_faa.extra_files_path"
59 --scaffold_dir "${GALAXY_DATA_INDEX_DIR}/plant_tribes/scaffolds" 60 --scaffold_dir "${GALAXY_DATA_INDEX_DIR}/plant_tribes/scaffolds"
60 --scaffold "$scaffold" 61 --scaffold "$scaffold"
61 --method $method 62 --method $method
62 63