diff parallel_blast.xml @ 0:e5c3175506b7 default tip

Initial tool configs for qiime, most need work.

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/parallel_blast.xml	Sun Jul 17 10:30:11 2011 -0500
@@ -0,0 +1,80 @@
+<tool id="parallel_blast" name="parallel_blast" version="1.2.0">
+ <description>Parallel BLAST</description>
+ <requirements>
+  <requirement type="binary">parallel_blast.py</requirement>
+ </requirements>
+ <command interpreter="python">
+  qiime_wrapper.py
+  --galaxy_tmpdir='$__new_file_path__'
+  parallel_blast.py
+  --infile_path=$infile_path
+  --refseqs_path=$refseqs_path
+  --output_dir=$__new_file_path__
+  $disable_low_complexity_filter
+  --e_value=$e_value
+  --num_hits=$num_hits
+  --word_size=$word_size
+  $suppress_format_blastdb
+  --blastmat_dir=$blastmat_dir
+  --blastall_fp=$blastall_fp
+  --jobs_to_start=$jobs_to_start
+  --poller_fp=$poller_fp
+  $retain_temp_files
+  $suppress_submit_jobs
+  $poll_directly
+  --cluster_jobs_fp=$cluster_jobs_fp
+  $suppress_polling
+  --job_prefix=$job_prefix
+  --python_exe_fp=$python_exe_fp
+  --seconds_to_sleep=$seconds_to_sleep
+ </command>
+ <inputs>
+  <param name="infile_path" type="text"  label="infile_path"
+   help="Path of sequences to use as queries [REQUIRED]"/>
+  <param name="refseqs_path" type="text"  label="refseqs_path"
+   help="Path to fasta sequences to search against [REQUIRED]"/>
+  <param name="disable_low_complexity_filter" type="boolean" truevalue="--disable_low_complexity_filter" falsevalue="" checked="false" label="disable_low_complexity_filter"
+   help="disable filtering of low-complexity sequences (i.e., -F F is passed to blast) [default: False]"/>
+  <param name="e_value" type="float" value="1e-30" label="e_value"
+   help="E-value threshold for blasts [default: 1e-30]"/>
+  <param name="num_hits" type="integer" value="1" label="num_hits"
+   help="number of hits per query for blast results [default: 1]"/>
+  <param name="word_size" type="integer" value="30" label="word_size"
+   help="word size for blast searches [default: 30]"/>
+  <param name="suppress_format_blastdb" type="boolean" truevalue="--suppress_format_blastdb" falsevalue="" checked="false" label="suppress_format_blastdb"
+   help="supress format of blastdb [default: False]"/>
+  <param name="blastmat_dir" type="text"  label="blastmat_dir"
+   help="full path to directory containing blastmat file [default: %default]"/>
+  <param name="blastall_fp" type="data" format="txt" label="blastall_fp"
+   help="Path to blastall [default: blastall]"/>
+  <param name="jobs_to_start" type="integer" value="1" label="jobs_to_start"
+   help="Number of jobs to start [default: 1]"/>
+  <param name="poller_fp" type="data" format="txt" label="poller_fp"
+   help="full path to qiime/parallel/poller.py [default: /usr/local/lib/python2.6/site-packages/scripts/poller.py]"/>
+  <param name="retain_temp_files" type="boolean" truevalue="--retain_temp_files" falsevalue="" checked="false" label="retain_temp_files"
+   help="retain temporary files after runs complete (useful for debugging) [default: False]"/>
+  <param name="suppress_submit_jobs" type="boolean" truevalue="--suppress_submit_jobs" falsevalue="" checked="false" label="suppress_submit_jobs"
+   help="Only split input and write commands file - don't submit jobs [default: False]"/>
+  <param name="poll_directly" type="boolean" truevalue="--poll_directly" falsevalue="" checked="false" label="poll_directly"
+   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]"/>
+  <param name="cluster_jobs_fp" type="data" format="txt" label="cluster_jobs_fp"
+   help="path to cluster_jobs.py script  [default: /usr/local/lib/python2.6/site-packages/scripts/start_parallel_jobs.py]"/>
+  <param name="suppress_polling" type="boolean" truevalue="--suppress_polling" falsevalue="" checked="false" label="suppress_polling"
+   help="suppress polling of jobs and merging of results upon completion [default: False]"/>
+  <param name="job_prefix" type="text"  label="job_prefix"
+   help="job prefix [default: descriptive prefix + random chars]"/>
+  <param name="python_exe_fp" type="data" format="txt" label="python_exe_fp"
+   help="full path to python executable [default: python]"/>
+  <param name="seconds_to_sleep" type="integer" value="60" label="seconds_to_sleep"
+   help="Number of seconds to sleep between checks for run  completion when polling runs [default: 60]"/>
+ </inputs>
+ <outputs>
+  
+ </outputs>
+ <tests>
+ </tests>
+ <help>
+  
+ </help>
+</tool>
+