--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/denoise.xml	Sun Jul 17 10:30:11 2011 -0500
@@ -0,0 +1,53 @@
+<tool id="denoise" name="denoise" version="1.2.0">
+ <description>Denoise a flowgram file</description>
+ <requirements>
+  <requirement type="binary">denoise.py</requirement>
+ </requirements>
+ <command interpreter="python">
+  qiime_wrapper.py
+  --galaxy_tmpdir='$__new_file_path__'
+  denoise.py
+  --input_file=$input_file
+  --fasta_file=$fasta_file
+  --output_dir=$__new_file_path__
+  --method=$method
+  $keep_intermediates
+  --cut-off=$cut_off
+  --precision=$precision
+  --num_cpus=$num_cpus
+  $force_overwrite
+  --map_fname=$map_fname
+  --primer=$primer
+ </command>
+ <inputs>
+  <param name="input_file" type="data" format="txt" label="input_file"
+   help="path to flowgram files (.sff.txt), comma separated [REQUIRED]"/>
+  <param name="fasta_file" type="data" format="fasta" label="fasta_file"
+   help="path to fasta file from split_libraries.py [REQUIRED]"/>
+  <param name="method" type="text" value="fast" label="method"
+   help="Method to use for denoising. Choice of pyronoise or fast [default: fast]"/>
+  <param name="keep_intermediates" type="boolean" truevalue="--keep_intermediates" falsevalue="" checked="false" label="keep_intermediates"
+   help="Do not delete intermediate files -- useful for debugging [default: False]"/>
+  <param name="cut_off" type="float" value="0.05" label="cut-off"
+   help="cut-off value (passed to pyroNoise) [default: 0.05]"/>
+  <param name="precision" type="float" value="15.0" label="precision"
+   help="precision (passed to pyroNoise)[default: 15.0]"/>
+  <param name="num_cpus" type="integer" value="1" label="num_cpus"
+   help="number of CPUs [default: 1]"/>
+  <param name="force_overwrite" type="boolean" truevalue="--force_overwrite" falsevalue="" checked="false" label="force_overwrite"
+   help="Overwrite files in output directory [default: False]"/>
+  <param name="map_fname" type="data" format="tabular" label="map_fname"
+   help="name of mapping file, Has to contain field LinkerPrimerSequence. [REQUIRED] when method is fast"/>
+  <param name="primer" type="text"  label="primer"
+   help="primer sequence [default: %default]"/>
+ </inputs>
+ <outputs>
+  
+ </outputs>
+ <tests>
+ </tests>
+ <help>
+  
+ </help>
+</tool>
+