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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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1 <tool id="parallel_assign_taxonomy_rdp" name="parallel_assign_taxonomy_rdp" version="1.2.0">
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2 <description>Parallel taxonomy assignment using RDP</description>
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3 <requirements>
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4 <requirement type="binary">parallel_assign_taxonomy_rdp.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='$__new_file_path__'
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9 parallel_assign_taxonomy_rdp.py
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10 --input_fasta_fp=$input_fasta_fp
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11 --output_dir=$__new_file_path__
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12 --rdp_classifier_fp=$rdp_classifier_fp
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13 --confidence=$confidence
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14 --assign_taxonomy_fp=$assign_taxonomy_fp
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15 --jobs_to_start=$jobs_to_start
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16 --poller_fp=$poller_fp
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17 $retain_temp_files
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18 $suppress_submit_jobs
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19 $poll_directly
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20 --cluster_jobs_fp=$cluster_jobs_fp
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21 $suppress_polling
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22 --job_prefix=$job_prefix
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23 --python_exe_fp=$python_exe_fp
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24 --seconds_to_sleep=$seconds_to_sleep
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25 </command>
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26 <inputs>
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27 <param name="input_fasta_fp" type="data" format="fasta" label="input_fasta_fp"
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28 help="full path to input_fasta_fp [REQUIRED]"/>
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29 <param name="rdp_classifier_fp" type="data" format="txt" label="rdp_classifier_fp"
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30 help="full path to rdp classifier jar file [default: %default]"/>
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31 <param name="confidence" type="float" value="0.8" label="confidence"
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32 help="Minimum confidence to record an assignment [default: 0.8]"/>
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33 <param name="assign_taxonomy_fp" type="data" format="txt" label="assign_taxonomy_fp"
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34 help="full path to scripts/assign_taxonomy.py [default: /usr/local/lib/python2.6/site-packages/scripts/assign_taxonomy.py]"/>
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35 <param name="jobs_to_start" type="integer" value="1" label="jobs_to_start"
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36 help="Number of jobs to start [default: 1]"/>
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37 <param name="poller_fp" type="data" format="txt" label="poller_fp"
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38 help="full path to qiime/parallel/poller.py [default: /usr/local/lib/python2.6/site-packages/scripts/poller.py]"/>
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39 <param name="retain_temp_files" type="boolean" truevalue="--retain_temp_files" falsevalue="" checked="false" label="retain_temp_files"
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40 help="retain temporary files after runs complete (useful for debugging) [default: False]"/>
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41 <param name="suppress_submit_jobs" type="boolean" truevalue="--suppress_submit_jobs" falsevalue="" checked="false" label="suppress_submit_jobs"
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42 help="Only split input and write commands file - don't submit jobs [default: False]"/>
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43 <param name="poll_directly" type="boolean" truevalue="--poll_directly" falsevalue="" checked="false" label="poll_directly"
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44 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]"/>
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45 <param name="cluster_jobs_fp" type="data" format="txt" label="cluster_jobs_fp"
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46 help="path to cluster_jobs.py script [default: /usr/local/lib/python2.6/site-packages/scripts/start_parallel_jobs.py]"/>
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47 <param name="suppress_polling" type="boolean" truevalue="--suppress_polling" falsevalue="" checked="false" label="suppress_polling"
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48 help="suppress polling of jobs and merging of results upon completion [default: False]"/>
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49 <param name="job_prefix" type="text" label="job_prefix"
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50 help="job prefix [default: descriptive prefix + random chars]"/>
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51 <param name="python_exe_fp" type="data" format="txt" label="python_exe_fp"
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52 help="full path to python executable [default: python]"/>
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53 <param name="seconds_to_sleep" type="integer" value="60" label="seconds_to_sleep"
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54 help="Number of seconds to sleep between checks for run completion when polling runs [default: 60]"/>
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55 </inputs>
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56 <outputs>
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57
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58 </outputs>
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59 <tests>
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60 </tests>
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61 <help>
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62
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63 </help>
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64 </tool>
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65