--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/chimera.xml	Thu May 21 03:58:09 2015 -0400
@@ -0,0 +1,135 @@
+<tool id="vsearch_chimera_detection" name="VSearch chimera detection" version="@VERSION@.0">
+    <description></description>
+    <macros>
+        <import>vsearch_macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="stdio" />
+    <expand macro="version_command" />
+    <command>
+<![CDATA[
+    vsearch
+        @GENERAL@
+        --abskew $abskew
+        --chimeras $outfile
+        --dn $dn
+        --mindiffs $mindiffs
+        --mindiv $mindiv
+        --minh $minh
+        --xn $xn
+        $self_param
+        $selfid_param
+        #if $detection_mode.detection_mode_select == 'denovo':
+            --uchime_denovo $detection_mode.infile_denovo
+        #else:
+            --uchime_ref $detection_mode.infile_reference
+            --db $detection_mode.db
+        #end if
+
+        #if 'nonchimeras' in str($outputs):
+            --nonchimeras $nonchimeras
+        #end if
+        #if 'uchimealns' in str($outputs):
+            --uchimealns $uchimealns
+        #end if
+        #if 'uchimeout' in str($outputs):
+            --uchimeout $uchimeout
+        #end if
+
+]]>
+    </command>
+    <inputs>
+        <conditional name="detection_mode">
+            <param name="detection_mode_select" type="select" label="Detect chimeras" help="">
+                <option value="denovo">de novo</option>
+                <option value="reference">using a reference database</option>
+            </param>
+            <when value="denovo">
+                <param name="infile_denovo" type="data" format="fasta" label="Select your FASTA file" help="(--uchime_denovo)" />
+            </when>
+            <when value="reference">
+                <param name="infile_reference" type="data" format="fasta" label="Select your FASTA file" help="(--uchime_ref)" />
+                <param name="db" type="data" format="fasta" label="Select your reference database" help="(--db)" />
+          </when>
+        </conditional>
+
+        <param name="abskew" type="float" value="2.0" label="Minimal abundance ratio of parent vs chimera"
+            help="(--abskew)"/>
+        <param name="dn" type="float" value="1.4" label="'no' vote pseudo count"
+            help="(--dn)"/>
+        <param name="xn" type="float" value="8.0" label="'no' vote weight"
+            help="(--xn)"/>
+        <param name="mindiffs" type="integer" value="3" label="Minimum number of differences in segment"
+            help="(--mindiffs)"/>
+        <param name="mindiv" type="float" value="0.8" label="Minimum divergence from closest parent"
+            help="(--mindiv)"/>
+        <param name="minh" type="float" value="0.28" label="Minimum score"
+            help="(--minh)"/>
+
+        <expand macro="self_and_selfid" />
+
+        <param name="outputs" type="select" multiple="True" optional="True"
+            label="Select output formats" help="(--qmask)">
+            <option value="nonchimeras">Non-chimeric sequences (--nonchimeras)</option>
+            <option value="uchimealns">Chimera alignments (--uchimealns)</option>
+            <option value="uchimeout">Chimera info to tab-separated (--uchimeout)</option>
+        </param>
+
+    </inputs>
+    <outputs>
+        <data name="outfile" format="fasta" label="${tool.name} on ${on_string}" />
+        <data name="nonchimeras" format="fasta" label="${tool.name} on ${on_string}: Non Chimera">
+            <filter>'nonchimeras' in outputs</filter>
+        </data>
+        <data name="uchimealns" format="fasta" label="${tool.name} on ${on_string}: Chimera Alignments">
+            <filter>'uchimealns' in outputs</filter>
+        </data>
+        <data name="uchimeout" format="tabular" label="${tool.name} on ${on_string}: Chimera Information">
+            <filter>'uchimeout' in outputs</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="detection_mode_select" value="denovo"/>
+            <param name="infile_denovo" value="PR2-18S-rRNA-V4.derep.fsa.bz2" ftype="fasta" />
+            <param name="outputs" value="uchimeout"/>
+            <output name="outfile" file="chimera_result1.fasta" ftype="fasta" />
+            <output name="uchimeout" file="chimera_uchimeout_result1.tabular" ftype="tabular" />
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+**What it does**
+
+Sequence chimera detection based on a different scoring functions.
+
+Chimera detection options
+  --abskew REAL               min abundance ratio of parent vs chimera (2.0)
+  --alignwidth INT            width of alignment in uchimealn output (80)
+  --chimeras FILENAME         output chimeric sequences to file
+  --db FILENAME               reference database for --uchime_ref
+  --dn REAL                   'no' vote pseudo-count (1.4)
+  --mindiffs INT              minimum number of differences in segment (3)
+  --mindiv REAL               minimum divergence from closest parent (0.8)
+  --minh REAL                 minimum score (0.28)
+  --nonchimeras FILENAME      output non-chimeric sequences to file
+  --self                      exclude identical labels for --uchime_ref
+  --selfid                    exclude identical sequences for --uchime_ref
+  --uchime_denovo FILENAME    detect chimeras de novo
+  --uchime_ref FILENAME       detect chimeras using a reference database
+  --uchimealns FILENAME       output chimera alignments to file
+  --uchimeout FILENAME        output to chimera info to tab-separated file
+  --uchimeout5                make output compatible with uchime version 5
+  --xn REAL                   'no' vote weight (8.0)
+
+@EXTERNAL_DOCUMENTATION@
+
+-------
+
+@REFERENCES@
+
+
+]]>
+    </help>
+    <expand macro="citations" />
+</tool>