--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/filter_alignment.xml	Sun Jul 17 10:30:11 2011 -0500
@@ -0,0 +1,43 @@
+<tool id="filter_alignment" name="filter_alignment" version="1.2.0">
+ <description>Filter sequence alignment by removing highly variable regions</description>
+ <requirements>
+  <requirement type="binary">filter_alignment.py</requirement>
+ </requirements>
+ <command interpreter="python">
+  qiime_wrapper.py
+  ## --galaxy_tmpdir='$__new_file_path__'
+  --galaxy_outputdir='$pfiltered_fasta.extra_files_path'
+  --galaxy_datasets='^\S+_pfiltered\.\S+$:'$pfiltered_fasta
+  filter_alignment.py
+  --input_fasta_file=$input_fasta_file
+  --output_dir='$pfiltered_fasta.extra_files_path'
+  --lane_mask_fp=$lane_mask_fp
+  $suppress_lane_mask_filter
+  --allowed_gap_frac=$allowed_gap_frac
+  $remove_outliers
+  --threshold=$threshold
+ </command>
+ <inputs>
+  <param name="input_fasta_file" type="data" format="align" label="input_fasta_file"
+   help="the input directory  [REQUIRED]"/>
+  <param name="lane_mask_fp" type="data" format="filter" label="lane_mask_fp"
+   help="path to lanemask file [default: %default]"/>
+  <param name="suppress_lane_mask_filter" type="boolean" truevalue="--suppress_lane_mask_filter" falsevalue="" checked="false" label="suppress_lane_mask_filter"
+   help="suppress lane mask filtering (necessary to turn off lane-mask-based filtering when a qiime_config default is  provided for --lane_mask_fp) [default: False]"/>
+  <param name="allowed_gap_frac" type="float" value="0.999999" label="allowed_gap_frac"
+   help="gap filter threshold, filters positions which are gaps in } allowed_gap_frac of the sequences [default: 0.999999]"/>
+  <param name="remove_outliers" type="boolean" truevalue="--remove_outliers" falsevalue="" checked="false" label="remove_outliers"
+   help="remove seqs very dissimilar to the alignment consensus (see --threshold).  [default: False]"/>
+  <param name="threshold" type="float" value="3.0" label="threshold"
+   help="with -r, remove seqs whose dissimilarity to the consensus sequence is approximately } x standard devaitions above the mean of the sequences [default: 3.0]"/>
+ </inputs>
+ <outputs>
+  <data format="align" name="pfiltered_fasta" label="${tool.name} on ${on_string}: pfiltered.fasta"/>
+ </outputs>
+ <tests>
+ </tests>
+ <help>
+  
+ </help>
+</tool>
+