Mercurial > repos > jjohnson > qiime
comparison parallel_assign_taxonomy_blast.xml @ 0:e5c3175506b7 default tip
Initial tool configs for qiime, most need work.
| author | Jim Johnson <jj@umn.edu> |
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| date | Sun, 17 Jul 2011 10:30:11 -0500 |
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| -1:000000000000 | 0:e5c3175506b7 |
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| 1 <tool id="parallel_assign_taxonomy_blast" name="parallel_assign_taxonomy_blast" version="1.2.0"> | |
| 2 <description>Parallel taxonomy assignment using BLAST</description> | |
| 3 <requirements> | |
| 4 <requirement type="binary">parallel_assign_taxonomy_blast.py</requirement> | |
| 5 </requirements> | |
| 6 <command interpreter="python"> | |
| 7 qiime_wrapper.py | |
| 8 --galaxy_tmpdir='$__new_file_path__' | |
| 9 parallel_assign_taxonomy_blast.py | |
| 10 --input_fasta_fp=$input_fasta_fp | |
| 11 --id_to_taxonomy_fp=$id_to_taxonomy_fp | |
| 12 --output_dir=$__new_file_path__ | |
| 13 --reference_seqs_fp=$reference_seqs_fp | |
| 14 --blast_db=$blast_db | |
| 15 --e_value=$e_value | |
| 16 --blastmat_dir=$blastmat_dir | |
| 17 --assign_taxonomy_fp=$assign_taxonomy_fp | |
| 18 --jobs_to_start=$jobs_to_start | |
| 19 --poller_fp=$poller_fp | |
| 20 $retain_temp_files | |
| 21 $suppress_submit_jobs | |
| 22 $poll_directly | |
| 23 --cluster_jobs_fp=$cluster_jobs_fp | |
| 24 $suppress_polling | |
| 25 --job_prefix=$job_prefix | |
| 26 --python_exe_fp=$python_exe_fp | |
| 27 --seconds_to_sleep=$seconds_to_sleep | |
| 28 </command> | |
| 29 <inputs> | |
| 30 <param name="input_fasta_fp" type="data" format="fasta" label="input_fasta_fp" | |
| 31 help="full path to input_fasta_fp [REQUIRED]"/> | |
| 32 <param name="id_to_taxonomy_fp" type="data" format="tabular" label="id_to_taxonomy_fp" | |
| 33 help="full path to id_to_taxonomy mapping file [REQUIRED]"/> | |
| 34 <param name="reference_seqs_fp" type="data" format="txt" label="reference_seqs_fp" | |
| 35 help="Ref seqs to blast against. Must provide either --blast_db or --reference_seqs_db for assignment with blast [default: ('NO', 'DEFAULT')]"/> | |
| 36 <param name="blast_db" type="text" label="blast_db" | |
| 37 help="Database to blast against. Must provide either --blast_db or --reference_seqs_db for assignment with blast [default: ('NO', 'DEFAULT')]"/> | |
| 38 <param name="e_value" type="float" value="0.001" label="e_value" | |
| 39 help="Maximum e-value to record an assignment, only used for blast method [default: 0.001]"/> | |
| 40 <param name="blastmat_dir" type="text" label="blastmat_dir" | |
| 41 help="full path to directory containing blastmat file [default: %default]"/> | |
| 42 <param name="assign_taxonomy_fp" type="data" format="txt" label="assign_taxonomy_fp" | |
| 43 help="full path to scripts/assign_taxonomy.py [default: /usr/local/lib/python2.6/site-packages/scripts/assign_taxonomy.py]"/> | |
| 44 <param name="jobs_to_start" type="integer" value="1" label="jobs_to_start" | |
| 45 help="Number of jobs to start [default: 1]"/> | |
| 46 <param name="poller_fp" type="data" format="txt" label="poller_fp" | |
| 47 help="full path to qiime/parallel/poller.py [default: /usr/local/lib/python2.6/site-packages/scripts/poller.py]"/> | |
| 48 <param name="retain_temp_files" type="boolean" truevalue="--retain_temp_files" falsevalue="" checked="false" label="retain_temp_files" | |
| 49 help="retain temporary files after runs complete (useful for debugging) [default: False]"/> | |
| 50 <param name="suppress_submit_jobs" type="boolean" truevalue="--suppress_submit_jobs" falsevalue="" checked="false" label="suppress_submit_jobs" | |
| 51 help="Only split input and write commands file - don't submit jobs [default: False]"/> | |
| 52 <param name="poll_directly" type="boolean" truevalue="--poll_directly" falsevalue="" checked="false" label="poll_directly" | |
| 53 help="Poll directly for job completion rather than running poller as a separate job. If -T is specified this script will not return until all jobs have completed. [default: False]"/> | |
| 54 <param name="cluster_jobs_fp" type="data" format="txt" label="cluster_jobs_fp" | |
| 55 help="path to cluster_jobs.py script [default: /usr/local/lib/python2.6/site-packages/scripts/start_parallel_jobs.py]"/> | |
| 56 <param name="suppress_polling" type="boolean" truevalue="--suppress_polling" falsevalue="" checked="false" label="suppress_polling" | |
| 57 help="suppress polling of jobs and merging of results upon completion [default: False]"/> | |
| 58 <param name="job_prefix" type="text" label="job_prefix" | |
| 59 help="job prefix [default: descriptive prefix + random chars]"/> | |
| 60 <param name="python_exe_fp" type="data" format="txt" label="python_exe_fp" | |
| 61 help="full path to python executable [default: python]"/> | |
| 62 <param name="seconds_to_sleep" type="integer" value="60" label="seconds_to_sleep" | |
| 63 help="Number of seconds to sleep between checks for run completion when polling runs [default: 60]"/> | |
| 64 </inputs> | |
| 65 <outputs> | |
| 66 | |
| 67 </outputs> | |
| 68 <tests> | |
| 69 </tests> | |
| 70 <help> | |
| 71 | |
| 72 </help> | |
| 73 </tool> | |
| 74 |