diff parallel_identify_chimeric_seqs.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_identify_chimeric_seqs.xml	Sun Jul 17 10:30:11 2011 -0500
@@ -0,0 +1,89 @@
+<tool id="parallel_identify_chimeric_seqs" name="parallel_identify_chimeric_seqs" version="1.2.0">
+ <description>Parallel chimera detection</description>
+ <requirements>
+  <requirement type="binary">parallel_identify_chimeric_seqs.py</requirement>
+ </requirements>
+ <command interpreter="python">
+  qiime_wrapper.py
+  --galaxy_tmpdir='$__new_file_path__'
+  parallel_identify_chimeric_seqs.py
+  --input_fasta_fp=$input_fasta_fp
+  --aligned_reference_seqs_fp=$aligned_reference_seqs_fp
+  --id_to_taxonomy_fp=$id_to_taxonomy_fp
+  --reference_seqs_fp=$reference_seqs_fp
+  --blast_db=$blast_db
+  --chimera_detection_method=$chimera_detection_method
+  --num_fragments=$num_fragments
+  --taxonomy_depth=$taxonomy_depth
+  --max_e_value=$max_e_value
+  --min_div_ratio=$min_div_ratio
+  --output_fp=$output_fp
+  --identify_chimeric_seqs_fp=$identify_chimeric_seqs_fp
+  --jobs_to_start=$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="path to the input fasta file [REQUIRED]"/>
+  <param name="aligned_reference_seqs_fp" type="data" format="txt" label="aligned_reference_seqs_fp"
+   help="Path to (Py)Nast aligned reference sequences. REQUIRED when method ChimeraSlayer [default: ('NO', 'DEFAULT')]"/>
+  <param name="id_to_taxonomy_fp" type="data" format="tabular" label="id_to_taxonomy_fp"
+   help="Path to tab-delimited file mapping sequences to assigned taxonomy. Each assigned taxonomy is provided as a comma-separated list. [default: ('NO', 'DEFAULT'); REQUIRED when method is blast_fragments]"/>
+  <param name="reference_seqs_fp" type="data" format="txt" label="reference_seqs_fp"
+   help="Path to reference sequences (used to build a blast db when method blast_fragments). [default: ('NO', 'DEFAULT'); REQUIRED when method blast_fragments if no blast_db is provided;]"/>
+  <param name="blast_db" type="text"  label="blast_db"
+   help="Database to blast against. Must provide either --blast_db or --reference_seqs_fp when method is blast_fragments [default: ('NO', 'DEFAULT')]"/>
+  <param name="chimera_detection_method" type="select" label="chimera_detection_method"
+   help="Chimera detection method. Choices: blast_fragments or ChimeraSlayer. [default:ChimeraSlayer]">
+    <option value="blast_fragments">blast_fragments</option>
+    <option value="ChimeraSlayer" selected="true">ChimeraSlayer</option>
+  </param>
+  <param name="num_fragments" type="integer" value="3" label="num_fragments"
+   help="Number of fragments to split sequences into (i.e., number of expected breakpoints + 1) [default: 3]"/>
+  <param name="taxonomy_depth" type="integer" value="4" label="taxonomy_depth"
+   help="Number of taxonomic divisions to consider when comparing taxonomy assignments [default: 4]"/>
+  <param name="max_e_value" type="float" value="1e-30" label="max_e_value"
+   help="Max e-value to assign taxonomy [default: 1e-30]"/>
+  <param name="min_div_ratio" type="float" value="0.0" label="min_div_ratio"
+   help="min divergence ratio (passed to ChimeraSlayer). If set to None uses ChimeraSlayer default value.  [default: %default]"/>
+  <param name="identify_chimeric_seqs_fp" type="data" format="txt" label="identify_chimeric_seqs_fp"
+   help="full path to scripts/identify_chimeric_seqs.py [default: /usr/local/lib/python2.6/site-packages/scripts/identify_chimeric_seqs.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/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>
+  <data format="txt" name="output_fp"/>
+ </outputs>
+ <tests>
+ </tests>
+ <help>
+  
+ </help>
+</tool>
+