--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/chimera.vsearch.xml	Tue Mar 20 22:09:26 2018 -0400
@@ -0,0 +1,155 @@
+<tool profile="16.07" id="mothur_chimera_vsearch" name="Chimera.vsearch" version="@WRAPPER_VERSION@.0">
+    <description>find potential chimeric sequences using vsearch</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements">
+        <requirement type="package" version="2.6.0">vsearch</requirement>
+    </expand>
+    <expand macro="stdio"/>
+    <expand macro="version_command"/>
+    <command><![CDATA[
+@SHELL_OPTIONS@
+
+## create symlinks to input datasets
+ln -s '$fasta' fasta.dat &&
+#if $template.source == "self":
+    ln -s '$template.count' template.count.dat &&
+    ln -s '$template.group' template.group.dat &&
+#elif $template.source == "names":
+    ln -s '$template.name' template.name.dat &&
+#else:
+    ln -s '$template.reference' template.reference.dat &&
+#end if
+
+echo 'chimera.vsearch(
+    fasta=fasta.dat,
+    #if $template.source == "self":
+        reference=self,
+        #if float($template.abskew) > 0:
+            abskew=$template.abskew,
+        #end if
+        #if $template.group:
+            group=template.group.dat,
+        #end if
+        #if $template.count:
+            count=template.count.dat,
+        #end if
+    #elif $template.source == "names":
+        name=template.name.dat,
+    #else:
+        reference=template.reference.dat,
+    #end if
+    minh=$minh,
+    mindiv=$mindiv,
+    xn=$xn,
+    dn=$dn,
+    dereplicate=$dereplicate,
+    mindiffs=$mindiffs,
+    processors='\${GALAXY_SLOTS:-8}'
+)'
+| sed 's/ //g'  ## mothur trips over whitespace
+| mothur
+| tee mothur.out.log
+2>&1  ## uchime component writes output to stderr
+&& cat *accnos
+    ]]></command>
+    <inputs>
+        <param argument="fasta" type="data" format="mothur.align,fasta" label="fasta - Candiate Aligned Sequences"/>
+        <conditional name="template">
+            <param name="source" type="select" label="Select Reference Template from">
+                <option value="hist">History</option>
+                <option value="ref">Cached Reference</option>
+                <option value="self">Self</option>
+                <option value="names">Use a names file</option>
+            </param>
+            <when value="ref">
+                <param argument="reference" type="select" label="reference - Select an alignment database">
+                    <options from_data_table="mothur_aligndb"/>
+                </param>
+            </when>
+            <when value="hist">
+                <param argument="reference" type="data" format="fasta" label="reference - Reference to align with"/>
+            </when>
+            <when value="self">
+                <param argument="abskew" type="float" value="1.9" label="abskew - Abundance skew" help="Abundance skew is: min [ abund(parent1), abund(parent2) ] / abund(query). Default 1.9"/>
+                <param argument="group" type="data" format="mothur.groups" optional="true" label="group - Sequences Name reference"
+                    help="use the more abundant sequences from the same sample to check the query sequence"/>
+                <param argument="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table"
+                    help="Generated by count.seqs. When you use a count file with group info and dereplicate=T, mothur will create a count table containing seqeunces after chimeras are removed."/>
+            </when>
+            <when value="names">
+                <param argument="name" type="data" format="mothur.names" label="name - Sequence names"/>
+            </when>
+        </conditional>
+        <param argument="dereplicate" type="boolean" falsevalue="false" truevalue="true" checked="false"
+            label="dereplicate - remove chimeric sequences from all groups?"
+            help="If parameter is false, then if one group finds the seqeunce to be chimeric, then all groups find it to be chimeric"/>
+        <param argument="minh" type="float" value="0.3" min="0" label="minh - mininum score to report chimera. Default 0.3"
+            help="Values from 0.1 to 5 might be reasonable. Lower values increase sensitivity but may report more false positives."/>
+        <param argument="mindiv" type="float" value="0.5" min="0" label="mindiv - minimum divergence ratio"
+            help="to ignore very close chimeras, increase mindiv to 1.0 or 2.0, to increase sensitivity decrease minh to 0.1. Default 0.5"/>
+        <param argument="xn" type="float" value="8.0" min="0" label="xn - weight of a no vote. Default 8.0"
+            help="Decreasing this weight to around 3 or 4 may give better performance on denoised data"/>
+        <param argument="dn" type="float" value="1.4" min="0" label="dn - pseudo-count prior on number of no votes"
+            help="Reasonable values are probably in the range from 0.2 to 2.0. Default 1.4"/>
+        <param argument="mindiffs" type="integer" value="3" min="0" label="minimum number of differences in segment"/>
+        <expand macro="param-savelog"/>
+    </inputs>
+    <outputs>
+        <expand macro="logfile-output"/>
+        <data name="vsearch.chimeras" format="txt" from_work_dir="fasta.*vsearch.chimeras" label="${tool.name} on ${on_string}: uchime.chimeras"/>
+        <data name="out_accnos" format="mothur.accnos" from_work_dir="fasta.*vsearch.accnos" label="${tool.name} on ${on_string}: uchime.accnos"/>
+    </outputs>
+    <tests>
+        <test><!-- de novo test with name file -->
+            <param name="fasta" value="stool_small.unique.fasta"/>
+            <param name="source" value="names"/>
+            <param name="name" value="stool_small.names"/>
+            <output name="vsearch.chimeras" file="stool_small.vsearch.chimeras" ftype="txt"/>
+            <output name="out_accnos" file="stool_small.denovo.vsearch.accnos" ftype="mothur.accnos"/>
+            <param name="savelog" value="true"/>
+            <expand macro="logfile-test"/>
+        </test>
+        <test><!-- de novo test with count table-->
+            <param name="fasta" value="stool_small.unique.fasta"/>
+            <param name="source" value="self"/>
+            <param name="count" value="stool_small.count_table"/>
+            <output name="vsearch.chimeras" file="stool_small.vsearch.chimeras" ftype="txt"/>
+            <output name="out_accnos" file="stool_small.denovo.vsearch.accnos" ftype="mothur.accnos"/>
+            <param name="savelog" value="true"/>
+            <expand macro="logfile-test"/>
+        </test>
+        <test><!-- test with reference file -->
+            <param name="fasta" value="stool_small.unique.fasta"/>
+            <param name="source" value="hist"/>
+            <param name="reference" value="stool_small.unique.fasta"/>
+            <output name="vsearch.chimeras" ftype="txt">
+                <assert_contents>
+                    <expand macro="test-chimera-format"/>
+                    <has_text text="F11Fcsw_12747"/>
+                </assert_contents>
+            </output>
+            <output name="out_accnos" ftype="mothur.accnos">
+                <assert_contents>
+                    <expand macro="test-accnos-format"/>
+                    <has_text text="F11Fcsw_23322"/>
+                </assert_contents>
+            </output>
+            <param name="savelog" value="true"/>
+            <expand macro="logfile-test"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+@MOTHUR_OVERVIEW@
+
+**Command Documentation**
+
+The chimera.vsearch_ command reads a fasta file and reference file and outputs potentially chimeric sequences.
+
+.. _chimera.vsearch: https://www.mothur.org/wiki/Chimera.vsearch
+
+    ]]></help>
+    <expand macro="citations"/>
+</tool>