--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/identify_chimeric_seqs.xml	Sun Jul 17 10:30:11 2011 -0500
@@ -0,0 +1,68 @@
+<tool id="identify_chimeric_seqs" name="identify_chimeric_seqs" version="1.2.0">
+ <description>Identify chimeric sequences in input FASTA file</description>
+ <requirements>
+  <requirement type="binary">identify_chimeric_seqs.py</requirement>
+ </requirements>
+ <command interpreter="python">
+  qiime_wrapper.py
+  identify_chimeric_seqs.py
+  --input_fasta_fp=$input_fasta_fp
+  #if $pick.chimera_detection_method == 'ChimeraSlayer':
+    --chimera_detection_method=$pick.chimera_detection_method
+    --aligned_reference_seqs_fp=$pick.aligned_reference_seqs_fp
+    --min_div_ratio=$pick.min_div_ratio
+    $pick.keep_intermediates
+  #elif $pick.chimera_detection_method == 'blast_fragments':
+    --chimera_detection_method=$pick.chimera_detection_method
+    --id_to_taxonomy_fp=$pick.id_to_taxonomy_fp
+    --reference_seqs_fp=$pick.reference_seqs_fp
+    --blast_db=$pick.blast_db
+    --num_fragments=$pick.num_fragments
+    --taxonomy_depth=$pick.taxonomy_depth
+    --max_e_value=$pick.max_e_value
+  #end if
+  --output_fp=$output_fp
+ </command>
+ <inputs>
+  <param name="input_fasta_fp" type="data" format="fasta" label="input_fasta_fp"
+   help="path to the input fasta file [REQUIRED]"/>
+  <conditional name="pick">
+   <param name="chimera_detection_method" type="select" label="chimera_detection_method"
+    help="Chimera detection method. Choices: blast_fragments or ChimeraSlayer. [default:ChimeraSlayer]">
+     <option value="blast_fragments">blast_fragments</option>
+     <option value="ChimeraSlayer" selected="true">ChimeraSlayer</option>
+   </param>
+   <when value="ChimeraSlayer">
+    <param name="aligned_reference_seqs_fp" type="data" format="txt" label="aligned_reference_seqs_fp"
+     help="Path to (Py)Nast aligned reference sequences. REQUIRED when method ChimeraSlayer [default: ('NO', 'DEFAULT')]"/>
+    <param name="min_div_ratio" type="float" value="0.0" label="min_div_ratio"
+     help="min divergence ratio (passed to ChimeraSlayer). If set to None uses ChimeraSlayer default value.  [default: %default]"/>
+    <param name="keep_intermediates" type="boolean" truevalue="--keep_intermediates" falsevalue="" checked="false" label="keep_intermediates"
+     help="Keep intermediate files, useful for debugging  [default: False]"/>
+   </when>
+   <when value="blast_fragments">
+    <param name="blast_db" type="text"  label="blast_db"
+     help="Database to blast against. Must provide either --blast_db or --reference_seqs_fp when method is blast_fragments [default: ('NO', 'DEFAULT')]"/>
+    <param name="reference_seqs_fp" type="data" format="txt" label="reference_seqs_fp"
+     help="Path to reference sequences (used to build a blast db when method blast_fragments). [default: ('NO', 'DEFAULT'); REQUIRED when method blast_fragments if no blast_db is provided;]"/>
+    <param name="id_to_taxonomy_fp" type="data" format="tabular" label="id_to_taxonomy_fp"
+     help="Path to tab-delimited file mapping sequences to assigned taxonomy. Each assigned taxonomy is provided as a comma-separated list. [default: ('NO', 'DEFAULT'); REQUIRED when method is blast_fragments]"/>
+    <param name="taxonomy_depth" type="integer" value="4" label="taxonomy_depth"
+     help="Number of taxonomic divisions to consider when comparing taxonomy assignments [default: 4]"/>
+    <param name="num_fragments" type="integer" value="3" label="num_fragments"
+     help="Number of fragments to split sequences into (i.e., number of expected breakpoints + 1) [default: 3]"/>
+    <param name="max_e_value" type="float" value="1e-30" label="max_e_value"
+     help="Max e-value to assign taxonomy [default: 1e-30]"/>
+   </when>
+  </conditional> <!-- pick -->
+ </inputs>
+ <outputs>
+  <data format="txt" name="output_fp" label="${tool.name} on ${on_string}: chimeras"/>
+ </outputs>
+ <tests>
+ </tests>
+ <help>
+  
+ </help>
+</tool>
+