view exclude_seqs_by_blast.xml @ 0:e5c3175506b7 default tip

Initial tool configs for qiime, most need work.

<tool id="exclude_seqs_by_blast" name="exclude_seqs_by_blast" version="1.2.0">
 <description>Exclude contaminated sequences using BLAST</description>
 <requirements>
  <requirement type="binary">exclude_seqs_by_blast.py</requirement>
 </requirements>
 <command interpreter="python">
  qiime_wrapper.py
  --galaxy_tmpdir='$__new_file_path__'
  exclude_seqs_by_blast.py
  --querydb=$querydb
  --subjectdb=$subjectdb
  --outputfilename=$outputfilename
  --e_value=$e_value
  --percent_aligned=$percent_aligned
  $no_clean
  --blastmatroot=$blastmatroot
  --working_dir=$working_dir
  --max_hits=$max_hits
  --word_size=$word_size
  $no_format_db
 </command>
 <inputs>
  <param name="querydb" type="text"  label="querydb"
   help="The path to a FASTA file containing query sequences [REQUIRED]"/>
  <param name="subjectdb" type="text"  label="subjectdb"
   help="The path to a FASTA file to BLAST against [REQUIRED]"/>
  <param name="e_value" type="float" value="1e-10" label="e_value"
   help="The e-value cutoff for blast queries [default: 1e-10]."/>
  <param name="percent_aligned" type="float" value="0.97" label="percent_aligned"
   help="The % alignment cutoff for blast queries [default: 0.97]."/>
  <param name="no_clean" type="boolean" truevalue="--no_clean" falsevalue="" checked="false" label="no_clean"
   help="If set, don't delete files generated by formatdb after running [default: False]."/>
  <param name="blastmatroot" type="text"  label="blastmatroot"
   help="Path to a folder containing blast matrices [default: %default]."/>
  <param name="working_dir" type="text" value="/tmp" label="working_dir"
   help="Working dir for BLAST [default: /tmp]."/>
  <param name="max_hits" type="integer" value="100" label="max_hits"
   help="Max hits parameter for BLAST. CAUTION: Because filtering on alignment percentage occurs after BLAST, a max hits value of 1 in combination with an alignment percent filter could miss valid contaminants. [default: 100]"/>
  <param name="word_size" type="integer" value="28" label="word_size"
   help="Word size to use for BLAST search [default: 28]"/>
  <param name="no_format_db" type="boolean" truevalue="--no_format_db" falsevalue="" checked="false" label="no_format_db"
   help="If this flag is specified, format_db will not be called on the subject database (formatdb will be set to False).  This is  useful if you have already formatted the database and a) it took a very long time or b) you want to run the script in parallel on the pre-formatted database [default: False]"/>
 </inputs>
 <outputs>
  <data format="txt" name="outputfilename"/>
 </outputs>
 <tests>
 </tests>
 <help>
  
 </help>
</tool>