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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_identify_chimeric_seqs" name="parallel_identify_chimeric_seqs" version="1.2.0">
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2 <description>Parallel chimera detection</description>
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3 <requirements>
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4 <requirement type="binary">parallel_identify_chimeric_seqs.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='$__new_file_path__'
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9 parallel_identify_chimeric_seqs.py
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10 --input_fasta_fp=$input_fasta_fp
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11 --aligned_reference_seqs_fp=$aligned_reference_seqs_fp
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12 --id_to_taxonomy_fp=$id_to_taxonomy_fp
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13 --reference_seqs_fp=$reference_seqs_fp
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14 --blast_db=$blast_db
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15 --chimera_detection_method=$chimera_detection_method
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16 --num_fragments=$num_fragments
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17 --taxonomy_depth=$taxonomy_depth
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18 --max_e_value=$max_e_value
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19 --min_div_ratio=$min_div_ratio
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20 --output_fp=$output_fp
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21 --identify_chimeric_seqs_fp=$identify_chimeric_seqs_fp
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22 --jobs_to_start=$jobs_to_start
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23 --poller_fp=$poller_fp
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24 $retain_temp_files
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25 $suppress_submit_jobs
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26 $poll_directly
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27 --cluster_jobs_fp=$cluster_jobs_fp
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28 $suppress_polling
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29 --job_prefix=$job_prefix
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30 --python_exe_fp=$python_exe_fp
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31 --seconds_to_sleep=$seconds_to_sleep
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32 </command>
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33 <inputs>
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34 <param name="input_fasta_fp" type="data" format="fasta" label="input_fasta_fp"
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35 help="path to the input fasta file [REQUIRED]"/>
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36 <param name="aligned_reference_seqs_fp" type="data" format="txt" label="aligned_reference_seqs_fp"
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37 help="Path to (Py)Nast aligned reference sequences. REQUIRED when method ChimeraSlayer [default: ('NO', 'DEFAULT')]"/>
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38 <param name="id_to_taxonomy_fp" type="data" format="tabular" label="id_to_taxonomy_fp"
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39 help="Path to tab-delimited file mapping sequences to assigned taxonomy. Each assigned taxonomy is provided as a comma-separated list. [default: ('NO', 'DEFAULT'); REQUIRED when method is blast_fragments]"/>
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40 <param name="reference_seqs_fp" type="data" format="txt" label="reference_seqs_fp"
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41 help="Path to reference sequences (used to build a blast db when method blast_fragments). [default: ('NO', 'DEFAULT'); REQUIRED when method blast_fragments if no blast_db is provided;]"/>
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42 <param name="blast_db" type="text" label="blast_db"
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43 help="Database to blast against. Must provide either --blast_db or --reference_seqs_fp when method is blast_fragments [default: ('NO', 'DEFAULT')]"/>
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44 <param name="chimera_detection_method" type="select" label="chimera_detection_method"
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45 help="Chimera detection method. Choices: blast_fragments or ChimeraSlayer. [default:ChimeraSlayer]">
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46 <option value="blast_fragments">blast_fragments</option>
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47 <option value="ChimeraSlayer" selected="true">ChimeraSlayer</option>
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48 </param>
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49 <param name="num_fragments" type="integer" value="3" label="num_fragments"
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50 help="Number of fragments to split sequences into (i.e., number of expected breakpoints + 1) [default: 3]"/>
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51 <param name="taxonomy_depth" type="integer" value="4" label="taxonomy_depth"
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52 help="Number of taxonomic divisions to consider when comparing taxonomy assignments [default: 4]"/>
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53 <param name="max_e_value" type="float" value="1e-30" label="max_e_value"
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54 help="Max e-value to assign taxonomy [default: 1e-30]"/>
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55 <param name="min_div_ratio" type="float" value="0.0" label="min_div_ratio"
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56 help="min divergence ratio (passed to ChimeraSlayer). If set to None uses ChimeraSlayer default value. [default: %default]"/>
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57 <param name="identify_chimeric_seqs_fp" type="data" format="txt" label="identify_chimeric_seqs_fp"
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58 help="full path to scripts/identify_chimeric_seqs.py [default: /usr/local/lib/python2.6/site-packages/scripts/identify_chimeric_seqs.py]"/>
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59 <param name="jobs_to_start" type="integer" value="1" label="jobs_to_start"
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60 help="Number of jobs to start [default: 1]"/>
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61 <param name="poller_fp" type="data" format="txt" label="poller_fp"
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62 help="full path to qiime/parallel/poller.py [default: /usr/local/lib/python2.6/site-packages/scripts/poller.py]"/>
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63 <param name="retain_temp_files" type="boolean" truevalue="--retain_temp_files" falsevalue="" checked="false" label="retain_temp_files"
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64 help="retain temporary files after runs complete (useful for debugging) [default: False]"/>
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65 <param name="suppress_submit_jobs" type="boolean" truevalue="--suppress_submit_jobs" falsevalue="" checked="false" label="suppress_submit_jobs"
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66 help="Only split input and write commands file - don't submit jobs [default: False]"/>
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67 <param name="poll_directly" type="boolean" truevalue="--poll_directly" falsevalue="" checked="false" label="poll_directly"
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68 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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69 <param name="cluster_jobs_fp" type="data" format="txt" label="cluster_jobs_fp"
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70 help="path to cluster_jobs.py script [default: /usr/local/lib/python2.6/site-packages/scripts/start_parallel_jobs.py]"/>
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71 <param name="suppress_polling" type="boolean" truevalue="--suppress_polling" falsevalue="" checked="false" label="suppress_polling"
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72 help="suppress polling of jobs and merging of results upon completion [default: False]"/>
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73 <param name="job_prefix" type="text" label="job_prefix"
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74 help="job prefix [default: descriptive prefix + random chars]"/>
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75 <param name="python_exe_fp" type="data" format="txt" label="python_exe_fp"
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76 help="full path to python executable [default: python]"/>
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77 <param name="seconds_to_sleep" type="integer" value="60" label="seconds_to_sleep"
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78 help="Number of seconds to sleep between checks for run completion when polling runs [default: 60]"/>
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79 </inputs>
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80 <outputs>
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81 <data format="txt" name="output_fp"/>
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82 </outputs>
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83 <tests>
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84 </tests>
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85 <help>
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86
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87 </help>
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88 </tool>
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89