--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/filter_fasta.xml	Sun Jul 17 10:30:11 2011 -0500
@@ -0,0 +1,41 @@
+<tool id="filter_fasta" name="filter_fasta" version="1.2.0">
+ <description>This script can be applied to remove sequences from a fasta file based on input criteria.</description>
+ <requirements>
+  <requirement type="binary">filter_fasta.py</requirement>
+ </requirements>
+ <command interpreter="python">
+  qiime_wrapper.py
+  --galaxy_tmpdir='$__new_file_path__'
+  filter_fasta.py
+  --input_fasta_fp=$input_fasta_fp
+  --output_fasta_fp=$output_fasta_fp
+  --otu_map=$otu_map
+  --seq_id_fp=$seq_id_fp
+  --subject_fasta_fp=$subject_fasta_fp
+  --seq_id_prefix=$seq_id_prefix
+  $negate
+ </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="otu_map" type="data" format="tabular" label="otu_map"
+   help="an OTU map where sequences ids are those which should be retained"/>
+  <param name="seq_id_fp" type="data" format="txt" label="seq_id_fp"
+   help="A list of sequence identifiers (or tab-delimited lines with a seq identifier in the first field) which should be retained"/>
+  <param name="subject_fasta_fp" type="data" format="fasta" label="subject_fasta_fp"
+   help="A fasta file where the seq ids should be retained."/>
+  <param name="seq_id_prefix" type="text"  label="seq_id_prefix"
+   help="keep seqs where seq_id starts with this prefix"/>
+  <param name="negate" type="boolean" truevalue="--negate" falsevalue="" checked="false" label="negate"
+   help="discard passed seq ids rather than keep passed seq ids [default: False]"/>
+ </inputs>
+ <outputs>
+  <data format="txt" name="output_fasta_fp"/>
+ </outputs>
+ <tests>
+ </tests>
+ <help>
+  
+ </help>
+</tool>
+