Mercurial > repos > jjohnson > qiime
comparison parallel_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_blast" name="parallel_blast" version="1.2.0"> | |
| 2 <description>Parallel BLAST</description> | |
| 3 <requirements> | |
| 4 <requirement type="binary">parallel_blast.py</requirement> | |
| 5 </requirements> | |
| 6 <command interpreter="python"> | |
| 7 qiime_wrapper.py | |
| 8 --galaxy_tmpdir='$__new_file_path__' | |
| 9 parallel_blast.py | |
| 10 --infile_path=$infile_path | |
| 11 --refseqs_path=$refseqs_path | |
| 12 --output_dir=$__new_file_path__ | |
| 13 $disable_low_complexity_filter | |
| 14 --e_value=$e_value | |
| 15 --num_hits=$num_hits | |
| 16 --word_size=$word_size | |
| 17 $suppress_format_blastdb | |
| 18 --blastmat_dir=$blastmat_dir | |
| 19 --blastall_fp=$blastall_fp | |
| 20 --jobs_to_start=$jobs_to_start | |
| 21 --poller_fp=$poller_fp | |
| 22 $retain_temp_files | |
| 23 $suppress_submit_jobs | |
| 24 $poll_directly | |
| 25 --cluster_jobs_fp=$cluster_jobs_fp | |
| 26 $suppress_polling | |
| 27 --job_prefix=$job_prefix | |
| 28 --python_exe_fp=$python_exe_fp | |
| 29 --seconds_to_sleep=$seconds_to_sleep | |
| 30 </command> | |
| 31 <inputs> | |
| 32 <param name="infile_path" type="text" label="infile_path" | |
| 33 help="Path of sequences to use as queries [REQUIRED]"/> | |
| 34 <param name="refseqs_path" type="text" label="refseqs_path" | |
| 35 help="Path to fasta sequences to search against [REQUIRED]"/> | |
| 36 <param name="disable_low_complexity_filter" type="boolean" truevalue="--disable_low_complexity_filter" falsevalue="" checked="false" label="disable_low_complexity_filter" | |
| 37 help="disable filtering of low-complexity sequences (i.e., -F F is passed to blast) [default: False]"/> | |
| 38 <param name="e_value" type="float" value="1e-30" label="e_value" | |
| 39 help="E-value threshold for blasts [default: 1e-30]"/> | |
| 40 <param name="num_hits" type="integer" value="1" label="num_hits" | |
| 41 help="number of hits per query for blast results [default: 1]"/> | |
| 42 <param name="word_size" type="integer" value="30" label="word_size" | |
| 43 help="word size for blast searches [default: 30]"/> | |
| 44 <param name="suppress_format_blastdb" type="boolean" truevalue="--suppress_format_blastdb" falsevalue="" checked="false" label="suppress_format_blastdb" | |
| 45 help="supress format of blastdb [default: False]"/> | |
| 46 <param name="blastmat_dir" type="text" label="blastmat_dir" | |
| 47 help="full path to directory containing blastmat file [default: %default]"/> | |
| 48 <param name="blastall_fp" type="data" format="txt" label="blastall_fp" | |
| 49 help="Path to blastall [default: blastall]"/> | |
| 50 <param name="jobs_to_start" type="integer" value="1" label="jobs_to_start" | |
| 51 help="Number of jobs to start [default: 1]"/> | |
| 52 <param name="poller_fp" type="data" format="txt" label="poller_fp" | |
| 53 help="full path to qiime/parallel/poller.py [default: /usr/local/lib/python2.6/site-packages/scripts/poller.py]"/> | |
| 54 <param name="retain_temp_files" type="boolean" truevalue="--retain_temp_files" falsevalue="" checked="false" label="retain_temp_files" | |
| 55 help="retain temporary files after runs complete (useful for debugging) [default: False]"/> | |
| 56 <param name="suppress_submit_jobs" type="boolean" truevalue="--suppress_submit_jobs" falsevalue="" checked="false" label="suppress_submit_jobs" | |
| 57 help="Only split input and write commands file - don't submit jobs [default: False]"/> | |
| 58 <param name="poll_directly" type="boolean" truevalue="--poll_directly" falsevalue="" checked="false" label="poll_directly" | |
| 59 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]"/> | |
| 60 <param name="cluster_jobs_fp" type="data" format="txt" label="cluster_jobs_fp" | |
| 61 help="path to cluster_jobs.py script [default: /usr/local/lib/python2.6/site-packages/scripts/start_parallel_jobs.py]"/> | |
| 62 <param name="suppress_polling" type="boolean" truevalue="--suppress_polling" falsevalue="" checked="false" label="suppress_polling" | |
| 63 help="suppress polling of jobs and merging of results upon completion [default: False]"/> | |
| 64 <param name="job_prefix" type="text" label="job_prefix" | |
| 65 help="job prefix [default: descriptive prefix + random chars]"/> | |
| 66 <param name="python_exe_fp" type="data" format="txt" label="python_exe_fp" | |
| 67 help="full path to python executable [default: python]"/> | |
| 68 <param name="seconds_to_sleep" type="integer" value="60" label="seconds_to_sleep" | |
| 69 help="Number of seconds to sleep between checks for run completion when polling runs [default: 60]"/> | |
| 70 </inputs> | |
| 71 <outputs> | |
| 72 | |
| 73 </outputs> | |
| 74 <tests> | |
| 75 </tests> | |
| 76 <help> | |
| 77 | |
| 78 </help> | |
| 79 </tool> | |
| 80 |