Mercurial > repos > jjohnson > qiime

annotate parallel_assign_taxonomy_blast.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_assign_taxonomy_blast" name="parallel_assign_taxonomy_blast" version="1.2.0">
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
2 <description>Parallel taxonomy assignment using BLAST</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_assign_taxonomy_blast.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='$__new_file_path__'
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
9 parallel_assign_taxonomy_blast.py
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
10 --input_fasta_fp=$input_fasta_fp
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
11 --id_to_taxonomy_fp=$id_to_taxonomy_fp
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
12 --output_dir=$__new_file_path__
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
13 --reference_seqs_fp=$reference_seqs_fp
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
14 --blast_db=$blast_db
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
15 --e_value=$e_value
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
16 --blastmat_dir=$blastmat_dir
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
17 --assign_taxonomy_fp=$assign_taxonomy_fp
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
18 --jobs_to_start=$jobs_to_start
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
19 --poller_fp=$poller_fp
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
20 $retain_temp_files
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
21 $suppress_submit_jobs
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
22 $poll_directly
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
23 --cluster_jobs_fp=$cluster_jobs_fp
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
24 $suppress_polling
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
25 --job_prefix=$job_prefix
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
26 --python_exe_fp=$python_exe_fp
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
27 --seconds_to_sleep=$seconds_to_sleep
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
28 </command>
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
29 <inputs>
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
30 <param name="input_fasta_fp" type="data" format="fasta" label="input_fasta_fp"
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
31 help="full path to input_fasta_fp [REQUIRED]"/>
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
32 <param name="id_to_taxonomy_fp" type="data" format="tabular" label="id_to_taxonomy_fp"
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
33 help="full path to id_to_taxonomy mapping file [REQUIRED]"/>
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
34 <param name="reference_seqs_fp" type="data" format="txt" label="reference_seqs_fp"
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
35 help="Ref seqs to blast against. Must provide either --blast_db or --reference_seqs_db for assignment with blast [default: ('NO', 'DEFAULT')]"/>
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
36 <param name="blast_db" type="text" label="blast_db"
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
37 help="Database to blast against. Must provide either --blast_db or --reference_seqs_db for assignment with blast [default: ('NO', 'DEFAULT')]"/>
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
38 <param name="e_value" type="float" value="0.001" label="e_value"
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
39 help="Maximum e-value to record an assignment, only used for blast method [default: 0.001]"/>
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
40 <param name="blastmat_dir" type="text" label="blastmat_dir"
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
41 help="full path to directory containing blastmat file [default: %default]"/>
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
42 <param name="assign_taxonomy_fp" type="data" format="txt" label="assign_taxonomy_fp"
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
43 help="full path to scripts/assign_taxonomy.py [default: /usr/local/lib/python2.6/site-packages/scripts/assign_taxonomy.py]"/>
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
44 <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
45 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
46 <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
47 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
48 <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
49 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
50 <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
51 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
52 <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
53 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
54 <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
55 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
56 <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
57 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
58 <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
59 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
60 <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
61 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
62 <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
63 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
64 </inputs>
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
65 <outputs>
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
66
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
67 </outputs>
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
68 <tests>
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
69 </tests>
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
70 <help>
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
71
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
72 </help>
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
73 </tool>
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
74