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