Mercurial > repos > jjohnson > qiime

annotate parallel_beta_diversity.xml @ 0:e5c3175506b7 default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Initial tool configs for qiime, most need work.
author Jim Johnson <jj@umn.edu>
date Sun, 17 Jul 2011 10:30:11 -0500
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
1 <tool id="parallel_beta_diversity" name="parallel_beta_diversity" version="1.2.0">
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
2 <description>Parallel beta diversity</description>
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
3 <requirements>
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
4 <requirement type="binary">parallel_beta_diversity.py</requirement>
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
5 </requirements>
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
6 <command interpreter="python">
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
7 qiime_wrapper.py
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
8 --galaxy_tmpdir='$__new_file_path__'
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
9 parallel_beta_diversity.py
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
10 --input_path=$input_path
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
11 --output_path=$output_path
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
12 --metrics=$metrics
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
13 --tree_path=$tree_path
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
14 --beta_diversity_fp=$beta_diversity_fp
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
15 --poller_fp=$poller_fp
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
16 $retain_temp_files
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
17 $suppress_submit_jobs
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
18 $poll_directly
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
19 --cluster_jobs_fp=$cluster_jobs_fp
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
20 $suppress_polling
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
21 --job_prefix=$job_prefix
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
22 --python_exe_fp=$python_exe_fp
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
23 --seconds_to_sleep=$seconds_to_sleep
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
24 --jobs_to_start=$jobs_to_start
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
25 $full_tree
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
26 </command>
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
27 <inputs>
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
28 <param name="input_path" type="text" label="input_path"
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
29 help="input path, must be directory [REQUIRED]"/>
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
30 <param name="metrics" type="text" label="metrics"
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
31 help="metrics to use [REQUIRED]"/>
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
32 <param name="tree_path" type="text" label="tree_path"
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
33 help="path to newick tree file, required for phylogenetic metrics [default: ('NO', 'DEFAULT')]"/>
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
34 <param name="beta_diversity_fp" type="data" format="txt" label="beta_diversity_fp"
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
35 help="full path to scripts/beta_diversity.py [default: /usr/local/lib/python2.6/site-packages/scripts/beta_diversity.py]"/>
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
36 <param name="poller_fp" type="data" format="txt" label="poller_fp"
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
37 help="full path to qiime/parallel/poller.py [default: /usr/local/lib/python2.6/site-packages/scripts/poller.py]"/>
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
38 <param name="retain_temp_files" type="boolean" truevalue="--retain_temp_files" falsevalue="" checked="false" label="retain_temp_files"
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
39 help="retain temporary files after runs complete (useful for debugging) [default: False]"/>
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
40 <param name="suppress_submit_jobs" type="boolean" truevalue="--suppress_submit_jobs" falsevalue="" checked="false" label="suppress_submit_jobs"
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
41 help="Only split input and write commands file - don't submit jobs [default: False]"/>
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
42 <param name="poll_directly" type="boolean" truevalue="--poll_directly" falsevalue="" checked="false" label="poll_directly"
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
43 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]"/>
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
44 <param name="cluster_jobs_fp" type="data" format="txt" label="cluster_jobs_fp"
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
45 help="path to cluster_jobs.py script [default: /usr/local/lib/python2.6/site-packages/scripts/start_parallel_jobs.py]"/>
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
46 <param name="suppress_polling" type="boolean" truevalue="--suppress_polling" falsevalue="" checked="false" label="suppress_polling"
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
47 help="suppress polling of jobs and merging of results upon completion [default: False]"/>
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
48 <param name="job_prefix" type="text" label="job_prefix"
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
49 help="job prefix [default: descriptive prefix + random chars]"/>
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
50 <param name="python_exe_fp" type="data" format="txt" label="python_exe_fp"
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
51 help="full path to python executable [default: python]"/>
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
52 <param name="seconds_to_sleep" type="integer" value="60" label="seconds_to_sleep"
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
53 help="Number of seconds to sleep between checks for run completion when polling runs [default: 60]"/>
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
54 <param name="jobs_to_start" type="integer" value="1" label="jobs_to_start"
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
55 help="Number of jobs to start [default: 1]"/>
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
56 <param name="full_tree" type="boolean" truevalue="--full_tree" falsevalue="" checked="false" label="full_tree"
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
57 help="By default, we first compute the intersection of the tree with the otus present in the otu table. pass -f if you already have a minimal tree, and this script will run faster"/>
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
58 </inputs>
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
59 <outputs>
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
60 <data format="txt" name="output_path"/>
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
61 </outputs>
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
62 <tests>
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
63 </tests>
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
64 <help>
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
65
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
66 </help>
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
67 </tool>
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
68