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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_pick_otus_uclust_ref" name="parallel_pick_otus_uclust_ref" version="1.2.1">
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2 <description>Parallel pick otus using uclust_ref</description>
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3 <requirements>
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4 <requirement type="binary">parallel_pick_otus_uclust_ref.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='$__new_file_path__'
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9 parallel_pick_otus_uclust_ref.py
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10 --input_fasta_fp=$input_fasta_fp
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11 --output_dir=$__new_file_path__
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12 --refseqs_fp=$refseqs_fp
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13 --similarity=$similarity
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14 $enable_rev_strand_match
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15 $optimal_uclust
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16 $exact_uclust
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17 --max_accepts=$max_accepts
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18 --max_rejects=$max_rejects
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19 --stepwords=$stepwords
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20 --word_length=$word_length
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21 $uclust_stable_sort
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22 $suppress_uclust_stable_sort
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23 $save_uc_files
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24 --pick_otus_fp=$pick_otus_fp
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25 --jobs_to_start=$jobs_to_start
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26 --poller_fp=$poller_fp
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27 $retain_temp_files
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28 $suppress_submit_jobs
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29 $poll_directly
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30 --cluster_jobs_fp=$cluster_jobs_fp
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31 $suppress_polling
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32 --job_prefix=$job_prefix
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33 --python_exe_fp=$python_exe_fp
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34 --seconds_to_sleep=$seconds_to_sleep
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35 </command>
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36 <inputs>
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37 <param name="input_fasta_fp" type="data" format="fasta" label="input_fasta_fp"
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38 help="full path to input_fasta_fp [REQUIRED]"/>
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39 <param name="refseqs_fp" type="data" format="txt" label="refseqs_fp"
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40 help="full path to reference collection [REQUIRED]"/>
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41 <param name="similarity" type="float" value="0.97" label="similarity"
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42 help="Sequence similarity threshold [default: 0.97]"/>
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43 <param name="enable_rev_strand_match" type="boolean" truevalue="--enable_rev_strand_match" falsevalue="" checked="false" label="enable_rev_strand_match"
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44 help="Enable reverse strand matching for uclust otu picking, will double the amount of memory used. [default: False]"/>
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45 <param name="optimal_uclust" type="boolean" truevalue="--optimal_uclust" falsevalue="" checked="false" label="optimal_uclust"
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46 help="Pass the --optimal flag to uclust for uclust otu picking. [default: False]"/>
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47 <param name="exact_uclust" type="boolean" truevalue="--exact_uclust" falsevalue="" checked="false" label="exact_uclust"
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48 help="Pass the --exact flag to uclust for uclust otu picking. [default: False]"/>
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49 <param name="max_accepts" type="integer" value="20" label="max_accepts"
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50 help="max_accepts value to uclust and uclust_ref [default: 20]"/>
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51 <param name="max_rejects" type="integer" value="500" label="max_rejects"
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52 help="max_rejects value to uclust and uclust_ref [default: 500]"/>
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53 <param name="stepwords" type="integer" value="20" label="stepwords"
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54 help="stepwords value to uclust and uclust_ref [default: 20]"/>
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55 <param name="word_length" type="integer" value="12" label="word_length"
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56 help="w value to uclust and uclust_ref [default: 12]"/>
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57 <param name="uclust_stable_sort" type="boolean" truevalue="--uclust_stable_sort" falsevalue="" checked="false" label="uclust_stable_sort"
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58 help="Deprecated: stable sort enabled by default, pass --uclust_suppress_stable_sort to disable [default: True]"/>
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59 <param name="suppress_uclust_stable_sort" type="boolean" truevalue="--suppress_uclust_stable_sort" falsevalue="" checked="false" label="suppress_uclust_stable_sort"
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60 help="Don't pass --stable-sort to uclust [default: False]"/>
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61 <param name="save_uc_files" type="boolean" truevalue="" falsevalue="--save_uc_files" checked="false" label="save_uc_files"
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62 help="Enable preservation of intermediate uclust (.uc) files that are used to generate clusters via uclust. [default: True]"/>
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63 <param name="pick_otus_fp" type="data" format="txt" label="pick_otus_fp"
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64 help="full path to scripts/pick_otus.py [default: /usr/local/bin/pick_otus.py]"/>
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65 <param name="jobs_to_start" type="integer" value="1" label="jobs_to_start"
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66 help="Number of jobs to start [default: 1]"/>
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67 <param name="poller_fp" type="data" format="txt" label="poller_fp"
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68 help="full path to qiime/parallel/poller.py [default: /usr/local/bin/poller.py]"/>
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69 <param name="retain_temp_files" type="boolean" truevalue="--retain_temp_files" falsevalue="" checked="false" label="retain_temp_files"
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70 help="retain temporary files after runs complete (useful for debugging) [default: False]"/>
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71 <param name="suppress_submit_jobs" type="boolean" truevalue="--suppress_submit_jobs" falsevalue="" checked="false" label="suppress_submit_jobs"
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72 help="Only split input and write commands file - don't submit jobs [default: False]"/>
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73 <param name="poll_directly" type="boolean" truevalue="--poll_directly" falsevalue="" checked="false" label="poll_directly"
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74 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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75 <param name="cluster_jobs_fp" type="data" format="txt" label="cluster_jobs_fp"
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76 help="path to cluster_jobs.py script [default: /usr/local/bin/start_parallel_jobs.py]"/>
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77 <param name="suppress_polling" type="boolean" truevalue="--suppress_polling" falsevalue="" checked="false" label="suppress_polling"
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78 help="suppress polling of jobs and merging of results upon completion [default: False]"/>
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79 <param name="job_prefix" type="text" label="job_prefix"
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80 help="job prefix [default: descriptive prefix + random chars]"/>
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81 <param name="python_exe_fp" type="data" format="txt" label="python_exe_fp"
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82 help="full path to python executable [default: python]"/>
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83 <param name="seconds_to_sleep" type="integer" value="60" label="seconds_to_sleep"
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84 help="Number of seconds to sleep between checks for run completion when polling runs [default: 60]"/>
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85 </inputs>
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86 <outputs>
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87
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88 </outputs>
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89 <tests>
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90 </tests>
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91 <help>
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92
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93 </help>
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94 </tool>
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95