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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_alpha_diversity" name="parallel_alpha_diversity" version="1.2.0">
2 <description>Parallel alpha diversity</description>
3 <requirements>
4 <requirement type="binary">parallel_alpha_diversity.py</requirement>
5 </requirements>
6 <command interpreter="python">
7 qiime_wrapper.py
8 --galaxy_tmpdir='$__new_file_path__'
9 parallel_alpha_diversity.py
10 --input_path=$input_path
11 --output_path=$output_path
12 --metrics=$metrics
13 --tree_path=$tree_path
14 --alpha_diversity_fp=$alpha_diversity_fp
15 --poller_fp=$poller_fp
16 $retain_temp_files
17 $suppress_submit_jobs
18 $poll_directly
19 --cluster_jobs_fp=$cluster_jobs_fp
20 $suppress_polling
21 --job_prefix=$job_prefix
22 --python_exe_fp=$python_exe_fp
23 --seconds_to_sleep=$seconds_to_sleep
24 --jobs_to_start=$jobs_to_start
25 </command>
26 <inputs>
27 <param name="input_path" type="text" label="input_path"
28 help="input path, must be directory [REQUIRED]"/>
29 <param name="metrics" type="text" label="metrics"
30 help="metrics to use, comma delimited [REQUIRED]"/>
31 <param name="tree_path" type="text" label="tree_path"
32 help="path to newick tree file, required for phylogenetic metrics [default: ('NO', 'DEFAULT')]"/>
33 <param name="alpha_diversity_fp" type="data" format="txt" label="alpha_diversity_fp"
34 help="full path to scripts/alpha_diversity.py [default: /usr/local/lib/python2.6/site-packages/scripts/alpha_diversity.py]"/>
35 <param name="poller_fp" type="data" format="txt" label="poller_fp"
36 help="full path to qiime/parallel/poller.py [default: /usr/local/lib/python2.6/site-packages/scripts/poller.py]"/>
37 <param name="retain_temp_files" type="boolean" truevalue="--retain_temp_files" falsevalue="" checked="false" label="retain_temp_files"
38 help="retain temporary files after runs complete (useful for debugging) [default: False]"/>
39 <param name="suppress_submit_jobs" type="boolean" truevalue="--suppress_submit_jobs" falsevalue="" checked="false" label="suppress_submit_jobs"
40 help="Only split input and write commands file - don't submit jobs [default: False]"/>
41 <param name="poll_directly" type="boolean" truevalue="--poll_directly" falsevalue="" checked="false" label="poll_directly"
42 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]"/>
43 <param name="cluster_jobs_fp" type="data" format="txt" label="cluster_jobs_fp"
44 help="path to cluster_jobs.py script [default: /usr/local/lib/python2.6/site-packages/scripts/start_parallel_jobs.py]"/>
45 <param name="suppress_polling" type="boolean" truevalue="--suppress_polling" falsevalue="" checked="false" label="suppress_polling"
46 help="suppress polling of jobs and merging of results upon completion [default: False]"/>
47 <param name="job_prefix" type="text" label="job_prefix"
48 help="job prefix [default: descriptive prefix + random chars]"/>
49 <param name="python_exe_fp" type="data" format="txt" label="python_exe_fp"
50 help="full path to python executable [default: python]"/>
51 <param name="seconds_to_sleep" type="integer" value="60" label="seconds_to_sleep"
52 help="Number of seconds to sleep between checks for run completion when polling runs [default: 60]"/>
53 <param name="jobs_to_start" type="integer" value="1" label="jobs_to_start"
54 help="Number of jobs to start [default: 1]"/>
55 </inputs>
56 <outputs>
57 <data format="txt" name="output_path"/>
58 </outputs>
59 <tests>
60 </tests>
61 <help>
62
63 </help>
64 </tool>
65