--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/parallel_pick_otus_uclust_ref.xml	Sun Jul 17 10:30:11 2011 -0500
@@ -0,0 +1,95 @@
+<tool id="parallel_pick_otus_uclust_ref" name="parallel_pick_otus_uclust_ref" version="1.2.1">
+ <description>Parallel pick otus using uclust_ref</description>
+ <requirements>
+  <requirement type="binary">parallel_pick_otus_uclust_ref.py</requirement>
+ </requirements>
+ <command interpreter="python">
+  qiime_wrapper.py
+  --galaxy_tmpdir='$__new_file_path__'
+  parallel_pick_otus_uclust_ref.py
+  --input_fasta_fp=$input_fasta_fp
+  --output_dir=$__new_file_path__
+  --refseqs_fp=$refseqs_fp
+  --similarity=$similarity
+  $enable_rev_strand_match
+  $optimal_uclust
+  $exact_uclust
+  --max_accepts=$max_accepts
+  --max_rejects=$max_rejects
+  --stepwords=$stepwords
+  --word_length=$word_length
+  $uclust_stable_sort
+  $suppress_uclust_stable_sort
+  $save_uc_files
+  --pick_otus_fp=$pick_otus_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="input_fasta_fp" type="data" format="fasta" label="input_fasta_fp"
+   help="full path to input_fasta_fp [REQUIRED]"/>
+  <param name="refseqs_fp" type="data" format="txt" label="refseqs_fp"
+   help="full path to reference collection [REQUIRED]"/>
+  <param name="similarity" type="float" value="0.97" label="similarity"
+   help="Sequence similarity threshold [default: 0.97]"/>
+  <param name="enable_rev_strand_match" type="boolean" truevalue="--enable_rev_strand_match" falsevalue="" checked="false" label="enable_rev_strand_match"
+   help="Enable reverse strand matching for uclust otu picking, will double the amount of memory used. [default: False]"/>
+  <param name="optimal_uclust" type="boolean" truevalue="--optimal_uclust" falsevalue="" checked="false" label="optimal_uclust"
+   help="Pass the --optimal flag to uclust for uclust otu picking. [default: False]"/>
+  <param name="exact_uclust" type="boolean" truevalue="--exact_uclust" falsevalue="" checked="false" label="exact_uclust"
+   help="Pass the --exact flag to uclust for uclust otu picking. [default: False]"/>
+  <param name="max_accepts" type="integer" value="20" label="max_accepts"
+   help="max_accepts value to uclust and uclust_ref [default: 20]"/>
+  <param name="max_rejects" type="integer" value="500" label="max_rejects"
+   help="max_rejects value to uclust and uclust_ref [default: 500]"/>
+  <param name="stepwords" type="integer" value="20" label="stepwords"
+   help="stepwords value to uclust and uclust_ref [default: 20]"/>
+  <param name="word_length" type="integer" value="12" label="word_length"
+   help="w value to uclust and uclust_ref [default: 12]"/>
+  <param name="uclust_stable_sort" type="boolean" truevalue="--uclust_stable_sort" falsevalue="" checked="false" label="uclust_stable_sort"
+   help="Deprecated: stable sort enabled by default, pass --uclust_suppress_stable_sort to disable [default: True]"/>
+  <param name="suppress_uclust_stable_sort" type="boolean" truevalue="--suppress_uclust_stable_sort" falsevalue="" checked="false" label="suppress_uclust_stable_sort"
+   help="Don't pass --stable-sort to uclust [default: False]"/>
+  <param name="save_uc_files" type="boolean" truevalue="" falsevalue="--save_uc_files" checked="false" label="save_uc_files"
+   help="Enable preservation of intermediate uclust (.uc) files that are used to generate clusters via uclust. [default: True]"/>
+  <param name="pick_otus_fp" type="data" format="txt" label="pick_otus_fp"
+   help="full path to scripts/pick_otus.py [default: /usr/local/bin/pick_otus.py]"/>
+  <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/bin/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/bin/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>
+