comparison parallel_multiple_rarefactions.xml @ 0:e5c3175506b7 default tip

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