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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_multiple_rarefactions" name="parallel_multiple_rarefactions" version="1.2.0">
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2 <description>Parallel multiple file rarefaction</description>
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3 <requirements>
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4 <requirement type="binary">parallel_multiple_rarefactions.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='$__new_file_path__'
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9 parallel_multiple_rarefactions.py
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10 --input_path=$input_path
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11 --output_path=$output_path
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12 --min=$min
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13 --max=$max
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14 --step=$step
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15 --num-reps=$num_reps
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16 $lineages_included
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17 --single_rarefaction_fp=$single_rarefaction_fp
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18 --poller_fp=$poller_fp
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19 $retain_temp_files
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20 $suppress_submit_jobs
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21 $poll_directly
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22 --cluster_jobs_fp=$cluster_jobs_fp
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23 $suppress_polling
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24 --job_prefix=$job_prefix
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25 --python_exe_fp=$python_exe_fp
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26 --seconds_to_sleep=$seconds_to_sleep
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27 --jobs_to_start=$jobs_to_start
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28 </command>
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29 <inputs>
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30 <param name="input_path" type="text" label="input_path"
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31 help="input filepath, (the otu table) [REQUIRED]"/>
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32 <param name="min" type="integer" value="-1" label="min"
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33 help="min seqs/sample [REQUIRED]"/>
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34 <param name="max" type="integer" value="-1" label="max"
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35 help="max seqs/sample (inclusive) [REQUIRED]"/>
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36 <param name="step" type="integer" value="-1" label="step"
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37 help="levels: min, min+step... for level {= max [REQUIRED]"/>
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38 <param name="num_reps" type="integer" value="1" label="num-reps"
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39 help="num iterations at each seqs/sample level [default: 1]"/>
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40 <param name="lineages_included" type="boolean" truevalue="--lineages_included" falsevalue="" checked="false" label="lineages_included"
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41 help="output rarefied otu tables will include taxonomic (lineage) information for each otu, if present in input otu table [default: False]"/>
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42 <param name="single_rarefaction_fp" type="data" format="txt" label="single_rarefaction_fp"
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43 help="full path to scripts/single_rarefaction.py [default: /usr/local/lib/python2.6/site-packages/scripts/single_rarefaction.py]"/>
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44 <param name="poller_fp" type="data" format="txt" label="poller_fp"
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45 help="full path to qiime/parallel/poller.py [default: /usr/local/lib/python2.6/site-packages/scripts/poller.py]"/>
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46 <param name="retain_temp_files" type="boolean" truevalue="--retain_temp_files" falsevalue="" checked="false" label="retain_temp_files"
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47 help="retain temporary files after runs complete (useful for debugging) [default: False]"/>
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48 <param name="suppress_submit_jobs" type="boolean" truevalue="--suppress_submit_jobs" falsevalue="" checked="false" label="suppress_submit_jobs"
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49 help="Only split input and write commands file - don't submit jobs [default: False]"/>
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50 <param name="poll_directly" type="boolean" truevalue="--poll_directly" falsevalue="" checked="false" label="poll_directly"
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51 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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52 <param name="cluster_jobs_fp" type="data" format="txt" label="cluster_jobs_fp"
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53 help="path to cluster_jobs.py script [default: /usr/local/lib/python2.6/site-packages/scripts/start_parallel_jobs.py]"/>
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54 <param name="suppress_polling" type="boolean" truevalue="--suppress_polling" falsevalue="" checked="false" label="suppress_polling"
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55 help="suppress polling of jobs and merging of results upon completion [default: False]"/>
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56 <param name="job_prefix" type="text" label="job_prefix"
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57 help="job prefix [default: descriptive prefix + random chars]"/>
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58 <param name="python_exe_fp" type="data" format="txt" label="python_exe_fp"
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59 help="full path to python executable [default: python]"/>
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60 <param name="seconds_to_sleep" type="integer" value="60" label="seconds_to_sleep"
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61 help="Number of seconds to sleep between checks for run completion when polling runs [default: 60]"/>
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62 <param name="jobs_to_start" type="integer" value="1" label="jobs_to_start"
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63 help="Number of jobs to start [default: 1]"/>
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64 </inputs>
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65 <outputs>
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66 <data format="txt" name="output_path"/>
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67 </outputs>
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68 <tests>
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69 </tests>
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70 <help>
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71
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72 </help>
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73 </tool>
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74