view parallel_blast.xml @ 0:e5c3175506b7 default tip

Initial tool configs for qiime, most need work.

<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>