Mercurial > repos > jjohnson > qiime
comparison poller.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="poller" name="poller" version="1.2.0"> | |
| 2 <description>Poller for parallel QIIME scripts.</description> | |
| 3 <requirements> | |
| 4 <requirement type="binary">poller.py</requirement> | |
| 5 </requirements> | |
| 6 <command interpreter="python"> | |
| 7 qiime_wrapper.py | |
| 8 --galaxy_tmpdir='$__new_file_path__' | |
| 9 poller.py | |
| 10 --check_run_complete_file=$check_run_complete_file | |
| 11 --check_run_complete_f=$check_run_complete_f | |
| 12 --process_run_results_f=$process_run_results_f | |
| 13 --process_run_results_file=$process_run_results_file | |
| 14 --clean_up_f=$clean_up_f | |
| 15 --clean_up_file=$clean_up_file | |
| 16 --time_to_sleep=$time_to_sleep | |
| 17 </command> | |
| 18 <inputs> | |
| 19 <param name="check_run_complete_file" type="data" format="txt" label="check_run_complete_file" | |
| 20 help="path to file containing a list of files that must exist to declare a run complete [REQUIRED]"/> | |
| 21 <param name="check_run_complete_f" type="text" value="qiime.parallel.poller.basic_check_run_complete_f" label="check_run_complete_f" | |
| 22 help="function which returns True when run is completed [default: qiime.parallel.poller.basic_check_run_complete_f]"/> | |
| 23 <param name="process_run_results_f" type="text" value="qiime.parallel.poller.basic_process_run_results_f" label="process_run_results_f" | |
| 24 help="function to be called when runs complete [default: qiime.parallel.poller.basic_process_run_results_f]"/> | |
| 25 <param name="process_run_results_file" type="data" format="tabular" label="process_run_results_file" | |
| 26 help="path to file containing a map of tmp filepaths which should be written to final output filepaths [default: ('NO', 'DEFAULT')]"/> | |
| 27 <param name="clean_up_f" type="text" value="qiime.parallel.poller.basic_clean_up_f" label="clean_up_f" | |
| 28 help="function called after processing result [default: qiime.parallel.poller.basic_clean_up_f]"/> | |
| 29 <param name="clean_up_file" type="data" format="txt" label="clean_up_file" | |
| 30 help="List of files and directories to remove after run [default: ('NO', 'DEFAULT')]"/> | |
| 31 <param name="time_to_sleep" type="integer" value="60" label="time_to_sleep" | |
| 32 help="time to wait between calls to status_callback_f (in seconds) [default: 60]"/> | |
| 33 </inputs> | |
| 34 <outputs> | |
| 35 | |
| 36 </outputs> | |
| 37 <tests> | |
| 38 </tests> | |
| 39 <help> | |
| 40 | |
| 41 </help> | |
| 42 </tool> | |
| 43 |