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Initial tool configs for qiime, most need work.
author Jim Johnson <jj@umn.edu>
date Sun, 17 Jul 2011 10:30:11 -0500
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e5c3175506b7 Initial tool configs for qiime, most need work.
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1 <tool id="poller" name="poller" version="1.2.0">
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2 <description>Poller for parallel QIIME scripts.</description>
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3 <requirements>
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4 <requirement type="binary">poller.py</requirement>
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5 </requirements>
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6 <command interpreter="python">
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7 qiime_wrapper.py
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8 --galaxy_tmpdir='$__new_file_path__'
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9 poller.py
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10 --check_run_complete_file=$check_run_complete_file
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11 --check_run_complete_f=$check_run_complete_f
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12 --process_run_results_f=$process_run_results_f
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13 --process_run_results_file=$process_run_results_file
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14 --clean_up_f=$clean_up_f
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15 --clean_up_file=$clean_up_file
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16 --time_to_sleep=$time_to_sleep
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17 </command>
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18 <inputs>
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19 <param name="check_run_complete_file" type="data" format="txt" label="check_run_complete_file"
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20 help="path to file containing a list of files that must exist to declare a run complete [REQUIRED]"/>
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21 <param name="check_run_complete_f" type="text" value="qiime.parallel.poller.basic_check_run_complete_f" label="check_run_complete_f"
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22 help="function which returns True when run is completed [default: qiime.parallel.poller.basic_check_run_complete_f]"/>
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23 <param name="process_run_results_f" type="text" value="qiime.parallel.poller.basic_process_run_results_f" label="process_run_results_f"
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24 help="function to be called when runs complete [default: qiime.parallel.poller.basic_process_run_results_f]"/>
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25 <param name="process_run_results_file" type="data" format="tabular" label="process_run_results_file"
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26 help="path to file containing a map of tmp filepaths which should be written to final output filepaths [default: ('NO', 'DEFAULT')]"/>
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27 <param name="clean_up_f" type="text" value="qiime.parallel.poller.basic_clean_up_f" label="clean_up_f"
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28 help="function called after processing result [default: qiime.parallel.poller.basic_clean_up_f]"/>
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29 <param name="clean_up_file" type="data" format="txt" label="clean_up_file"
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30 help="List of files and directories to remove after run [default: ('NO', 'DEFAULT')]"/>
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31 <param name="time_to_sleep" type="integer" value="60" label="time_to_sleep"
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32 help="time to wait between calls to status_callback_f (in seconds) [default: 60]"/>
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33 </inputs>
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34 <outputs>
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35
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36 </outputs>
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37 <tests>
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38 </tests>
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39 <help>
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40
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41 </help>
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42 </tool>
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43