--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/filter_fasta.xml	Tue Feb 02 05:50:37 2016 -0500
@@ -0,0 +1,102 @@
+<tool id="qiime_filter_fasta" name="filter fasta" version="1.9.1galaxy1">
+    <description>This script can be applied to remove sequences from a fasta or 
+        fastq file based on input criteria.</description>
+
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+
+    <expand macro="requirements" />
+
+    <command>
+<![CDATA[        
+        filter_fasta.py 
+            -f $input_fasta_fp 
+            -o $output_fasta_fp
+            #if str($otu_map) != 'None':
+             -m $otu_map
+            #end if
+
+            #if str($seq_id_fp) != 'None':
+             -s $seq_id_fp
+            #end if
+
+            #if str($biom_fp) != 'None':
+             -b $biom_fp
+            #end if
+
+            #if str($subject_fasta_fp) != 'None':
+             -a $subject_fasta_fp
+            #end if
+
+            #if str($seq_id_prefix):
+             -p $seq_id_prefix
+            #end if
+
+            #if str($sample_id_fp) != 'None':
+             --sample_id_fp=$sample_id_fp
+            #end if
+
+            #if $negate:
+             -n
+            #end if
+
+            #if str($mapping_fp) != 'None':
+             --mapping_fp=$mapping_fp
+            #end if
+
+            #if str($valid_states):
+             --valid_states=$valid_states
+            #end if
+]]>
+    </command>
+
+    <inputs>
+        <param label="-f/--input_fasta_fp: path to the input fasta file" 
+            name="input_fasta_fp" optional="False" type="data"/>
+        <param label="-m/--otu_map: an OTU map where sequences ids are those 
+            which should be retained" name="otu_map" optional="True" type="data"/>
+        <param label="-s/--seq_id_fp: A list of sequence identifiers (or tab-delimited 
+            lines with a seq identifier in the first field) which should be retained" 
+            name="seq_id_fp" optional="True" type="data"/>
+        <param label="-b/--biom_fp: A biom file where otu identifiers should be 
+            retained" name="biom_fp" optional="True" type="data"/>
+        <param label="-a/--subject_fasta_fp: A fasta file where the seq ids should 
+            be retained." name="subject_fasta_fp" optional="True" type="data"/>
+        <param label="-p/--seq_id_prefix: keep seqs where seq_id starts with this 
+            prefix" name="seq_id_prefix" optional="True" type="text"/>
+        <param label="--sample_id_fp: keep seqs where seq_id starts with a sample 
+            id listed in this file" name="sample_id_fp" optional="True" 
+            type="data"/>
+        <param label="-n/--negate: discard passed seq ids rather than keep passed 
+            seq ids [default: False]" name="negate" selected="False" 
+            type="boolean"/>
+        <param label="--mapping_fp: mapping file path (for use with --valid_states) 
+            [default: None]" name="mapping_fp" optional="True" type="data"/>
+        <param label="--valid_states: description of sample ids to retain (for use 
+            with --mapping_fp) [default: None]" name="valid_states" optional="True" 
+            type="text"/>
+    </inputs>
+
+    <outputs>
+        <data format="txt" name="output_fasta_fp"/>
+    </outputs>
+
+    <tests>
+        <test>
+        </test>
+    </tests>
+
+    <help>
+<![CDATA[
+
+**What it does**
+
+
+    ]]>
+    </help>
+
+    <citations>
+        <expand macro="citations" />
+    </citations>
+</tool>