--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/exclude_seqs_by_blast.xml	Sun Jul 17 10:30:11 2011 -0500
@@ -0,0 +1,53 @@
+<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>
+