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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_align_seqs_pynast" name="parallel_align_seqs_pynast" version="1.2.0">
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2 <description>Parallel sequence alignment using PyNAST</description>
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3 <requirements>
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4 <requirement type="binary">parallel_align_seqs_pynast.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='$__new_file_path__'
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9 parallel_align_seqs_pynast.py
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10 --input_fasta_fp=$input_fasta_fp
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11 --output_dir=$__new_file_path__
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12 --template_fp=$template_fp
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13 --pairwise_alignment_method=$pairwise_alignment_method
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14 --blast_db=$blast_db
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15 --min_length=$min_length
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16 --min_percent_id=$min_percent_id
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17 --align_seqs_fp=$align_seqs_fp
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18 --jobs_to_start=$jobs_to_start
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19 --poller_fp=$poller_fp
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20 $retain_temp_files
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21 $suppress_submit_jobs
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22 $poll_directly
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23 --cluster_jobs_fp=$cluster_jobs_fp
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24 $suppress_polling
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25 --job_prefix=$job_prefix
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26 --python_exe_fp=$python_exe_fp
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27 --seconds_to_sleep=$seconds_to_sleep
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28 </command>
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29 <inputs>
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30 <param name="input_fasta_fp" type="data" format="fasta" label="input_fasta_fp"
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31 help="path to the input fasta file [REQUIRED]"/>
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32 <param name="template_fp" type="data" format="txt" label="template_fp"
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33 help="Filepath for template against [REQUIRED]"/>
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34 <param name="pairwise_alignment_method" type="select" label="pairwise_alignment_method"
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35 help="Method to use for pairwise alignments [default: uclust]">
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36 <option value="muscle">muscle</option>
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37 <option value="pair_hmm">pair_hmm</option>
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38 <option value="clustal">clustal</option>
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39 <option value="blast">blast</option>
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40 <option value="uclust" selected="true">uclust</option>
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41 <option value="mafft">mafft</option>
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42 </param>
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43 <param name="blast_db" type="text" label="blast_db"
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44 help="Database to blast against [default: created on-the-fly from template_alignment]"/>
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45 <param name="min_length" type="integer" value="150" label="min_length"
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46 help="Minimum sequence length to include in alignment [default: 150]"/>
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47 <param name="min_percent_id" type="float" value="75.0" label="min_percent_id"
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48 help="Minimum percent sequence identity to closest blast hit to include sequence in alignment [default: 75.0]"/>
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49 <param name="align_seqs_fp" type="data" format="txt" label="align_seqs_fp"
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50 help="full path to Qiime/scripts/align_seqs.py [default: /usr/local/lib/python2.6/site-packages/scripts/align_seqs.py]"/>
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51 <param name="jobs_to_start" type="integer" value="1" label="jobs_to_start"
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52 help="Number of jobs to start [default: 1]"/>
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53 <param name="poller_fp" type="data" format="txt" label="poller_fp"
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54 help="full path to qiime/parallel/poller.py [default: /usr/local/lib/python2.6/site-packages/scripts/poller.py]"/>
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55 <param name="retain_temp_files" type="boolean" truevalue="--retain_temp_files" falsevalue="" checked="false" label="retain_temp_files"
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56 help="retain temporary files after runs complete (useful for debugging) [default: False]"/>
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57 <param name="suppress_submit_jobs" type="boolean" truevalue="--suppress_submit_jobs" falsevalue="" checked="false" label="suppress_submit_jobs"
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58 help="Only split input and write commands file - don't submit jobs [default: False]"/>
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59 <param name="poll_directly" type="boolean" truevalue="--poll_directly" falsevalue="" checked="false" label="poll_directly"
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60 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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61 <param name="cluster_jobs_fp" type="data" format="txt" label="cluster_jobs_fp"
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62 help="path to cluster_jobs.py script [default: /usr/local/lib/python2.6/site-packages/scripts/start_parallel_jobs.py]"/>
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63 <param name="suppress_polling" type="boolean" truevalue="--suppress_polling" falsevalue="" checked="false" label="suppress_polling"
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64 help="suppress polling of jobs and merging of results upon completion [default: False]"/>
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65 <param name="job_prefix" type="text" label="job_prefix"
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66 help="job prefix [default: descriptive prefix + random chars]"/>
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67 <param name="python_exe_fp" type="data" format="txt" label="python_exe_fp"
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68 help="full path to python executable [default: python]"/>
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69 <param name="seconds_to_sleep" type="integer" value="60" label="seconds_to_sleep"
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70 help="Number of seconds to sleep between checks for run completion when polling runs [default: 60]"/>
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71 </inputs>
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72 <outputs>
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73
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74 </outputs>
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75 <tests>
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76 </tests>
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77 <help>
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78
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79 </help>
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80 </tool>
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81