Mercurial > repos > jjohnson > qiime
comparison parallel_beta_diversity.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_beta_diversity" name="parallel_beta_diversity" version="1.2.0"> | |
| 2 <description>Parallel beta diversity</description> | |
| 3 <requirements> | |
| 4 <requirement type="binary">parallel_beta_diversity.py</requirement> | |
| 5 </requirements> | |
| 6 <command interpreter="python"> | |
| 7 qiime_wrapper.py | |
| 8 --galaxy_tmpdir='$__new_file_path__' | |
| 9 parallel_beta_diversity.py | |
| 10 --input_path=$input_path | |
| 11 --output_path=$output_path | |
| 12 --metrics=$metrics | |
| 13 --tree_path=$tree_path | |
| 14 --beta_diversity_fp=$beta_diversity_fp | |
| 15 --poller_fp=$poller_fp | |
| 16 $retain_temp_files | |
| 17 $suppress_submit_jobs | |
| 18 $poll_directly | |
| 19 --cluster_jobs_fp=$cluster_jobs_fp | |
| 20 $suppress_polling | |
| 21 --job_prefix=$job_prefix | |
| 22 --python_exe_fp=$python_exe_fp | |
| 23 --seconds_to_sleep=$seconds_to_sleep | |
| 24 --jobs_to_start=$jobs_to_start | |
| 25 $full_tree | |
| 26 </command> | |
| 27 <inputs> | |
| 28 <param name="input_path" type="text" label="input_path" | |
| 29 help="input path, must be directory [REQUIRED]"/> | |
| 30 <param name="metrics" type="text" label="metrics" | |
| 31 help="metrics to use [REQUIRED]"/> | |
| 32 <param name="tree_path" type="text" label="tree_path" | |
| 33 help="path to newick tree file, required for phylogenetic metrics [default: ('NO', 'DEFAULT')]"/> | |
| 34 <param name="beta_diversity_fp" type="data" format="txt" label="beta_diversity_fp" | |
| 35 help="full path to scripts/beta_diversity.py [default: /usr/local/lib/python2.6/site-packages/scripts/beta_diversity.py]"/> | |
| 36 <param name="poller_fp" type="data" format="txt" label="poller_fp" | |
| 37 help="full path to qiime/parallel/poller.py [default: /usr/local/lib/python2.6/site-packages/scripts/poller.py]"/> | |
| 38 <param name="retain_temp_files" type="boolean" truevalue="--retain_temp_files" falsevalue="" checked="false" label="retain_temp_files" | |
| 39 help="retain temporary files after runs complete (useful for debugging) [default: False]"/> | |
| 40 <param name="suppress_submit_jobs" type="boolean" truevalue="--suppress_submit_jobs" falsevalue="" checked="false" label="suppress_submit_jobs" | |
| 41 help="Only split input and write commands file - don't submit jobs [default: False]"/> | |
| 42 <param name="poll_directly" type="boolean" truevalue="--poll_directly" falsevalue="" checked="false" label="poll_directly" | |
| 43 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]"/> | |
| 44 <param name="cluster_jobs_fp" type="data" format="txt" label="cluster_jobs_fp" | |
| 45 help="path to cluster_jobs.py script [default: /usr/local/lib/python2.6/site-packages/scripts/start_parallel_jobs.py]"/> | |
| 46 <param name="suppress_polling" type="boolean" truevalue="--suppress_polling" falsevalue="" checked="false" label="suppress_polling" | |
| 47 help="suppress polling of jobs and merging of results upon completion [default: False]"/> | |
| 48 <param name="job_prefix" type="text" label="job_prefix" | |
| 49 help="job prefix [default: descriptive prefix + random chars]"/> | |
| 50 <param name="python_exe_fp" type="data" format="txt" label="python_exe_fp" | |
| 51 help="full path to python executable [default: python]"/> | |
| 52 <param name="seconds_to_sleep" type="integer" value="60" label="seconds_to_sleep" | |
| 53 help="Number of seconds to sleep between checks for run completion when polling runs [default: 60]"/> | |
| 54 <param name="jobs_to_start" type="integer" value="1" label="jobs_to_start" | |
| 55 help="Number of jobs to start [default: 1]"/> | |
| 56 <param name="full_tree" type="boolean" truevalue="--full_tree" falsevalue="" checked="false" label="full_tree" | |
| 57 help="By default, we first compute the intersection of the tree with the otus present in the otu table. pass -f if you already have a minimal tree, and this script will run faster"/> | |
| 58 </inputs> | |
| 59 <outputs> | |
| 60 <data format="txt" name="output_path"/> | |
| 61 </outputs> | |
| 62 <tests> | |
| 63 </tests> | |
| 64 <help> | |
| 65 | |
| 66 </help> | |
| 67 </tool> | |
| 68 |