--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/chimera.slayer.xml	Fri May 19 05:42:41 2017 -0400
@@ -0,0 +1,169 @@
+<tool profile="16.07" id="mothur_chimera_slayer" name="Chimera.slayer" version="@WRAPPER_VERSION@.0">
+    <description>Find putative chimeras using slayer</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
+    <expand macro="version_command"/>
+    <command><![CDATA[
+        @SHELL_OPTIONS@
+
+        ## enable mothur to find blast
+        loc=`which mothur` && ln -s "\${loc%/mothur}"/* . &&
+
+        ## create symlinks to input datasets
+        ln -s "$fasta" fasta.dat &&
+        #if $alignment.source == "self":
+            ln -s "$alignment.name" alignment.name.dat &&
+            ln -s "$alignment.group" alignment.group.dat &&
+            ln -s "$alignment.count" alignment.count.dat &&
+        #else:
+            ln -s "$alignment.template" alignment.template.dat &&
+        #end if
+
+        echo 'chimera.slayer(
+            fasta=fasta.dat,
+            #if $alignment.source == "self":
+                reference=self,
+                #if $alignment.name:
+                    name=$alignment.name,
+                #end if
+                #if $alignment.group:
+                    group=$alignment.group,
+                #end if
+                #if $alignment.count:
+                    count=$alignment.count,
+                #end if
+            #else:
+                reference=$alignment.template,
+            #end if
+            #if $options.setby == "user":
+                search=$options.search,
+                window=$options.window,
+                increment=$options.increment,
+                match=$options.match,
+                mismatch=$options.mismatch,
+                numwanted=$options.numwanted,
+                parents=$options.parents,
+                minsim=$options.minsim,
+                mincov=$options.mincov,
+                iters=$options.iters,
+                minbs=$options.minbs,
+                minsnp=$options.minsnp,
+                divergence=$options.divergence,
+                trim=$options.trim,
+                split=$options.split,
+            #end if
+            dereplicate=$dereplicate,
+            processors='\${GALAXY_SLOTS:-8}'
+        )'
+        | sed 's/ //g'  ## mothur trips over whitespace
+        | ./mothur
+        | tee mothur.out.log
+    ]]></command>
+    <inputs>
+        <param name="fasta" type="data" format="fasta" label="fasta - Candiate Sequences"/>
+        <conditional name="alignment">
+            <param name="source" type="select" label="Select Reference Template from" help="">
+                <option value="hist">History</option>
+                <option value="ref">Cached Reference</option>
+                <option value="self">Self - Use abundant sequences from the input Candiate Sequences fasta </option>
+            </param>
+            <when value="ref">
+                <param name="template" type="select" label="reference - Select an alignment database " help="">
+                    <options from_data_table="mothur_aligndb">
+                    </options>
+                </param>
+            </when>
+            <when value="hist">
+                <param name="template" type="data" format="fasta" label="reference - Reference to align with" help=""/>
+            </when>
+            <when value="self">
+                <param name="count" type="data" format="mothur.count_table" optional="true" label="count - Count file"/>
+                <param name="name" type="data" format="mothur.names" optional="true" label="names - Sequences Names"/>
+                <param name="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"/>
+            </when>
+        </conditional>
+        <conditional name="options">
+            <param name="setby" type="select" label="Slayer Options" help="">
+                <option value="default">Use default settings</option>
+                <option value="user">Manually set options</option>
+            </param>
+            <when value="default"/>
+            <when value="user">
+                <param name="search" type="select" label="search - Search method for finding the closest parent" help="">
+                    <option value="blast" selected="true">blast</option>
+                    <option value="kmer">kmer</option>
+                </param>
+                <param name="window" type="integer" value="50" label="window - Window size for searching for chimeras (default 50)"/>
+                <param name="increment" type="integer" value="5" label="increment - Increment for window slide on each iteration (default 5)"/>
+                <param name="match" type="integer" value="5" label="match - Reward matched bases (default 5)"/>
+                <param name="mismatch" type="integer" value="-4" label="mismatch - Penalty for mismatched bases (default -4)"/>
+                <param name="numwanted" type="integer" value="15" label="numwanted - Number of potential parents to to compare with query sequence (default 15)"/>
+                <param name="parents" type="integer" value="3" label="parents - Number of potential parents to investigate from the numwanted best matches"/>
+                <param name="minsim" type="integer" value="90" label="minsim - Minimum similarity % between the query and parent (default 90)"/>
+                <param name="mincov" type="integer" value="70" label="mincov - Minimum coverage % of closest matches in reference and the query (default 70)"/>
+                <param name="iters" type="integer" value="1000" label="iters - Number of bootstrap iterations to try (default 100)"/>
+                <param name="minbs" type="integer" value="90" label="minbs - Minimum bootstrap support % for calling a sequence chimeric (default 90)"/>
+                <param name="minsnp" type="integer" value="10" label="minsnp - Percent of SNPs to sample on each side of breakpoint for computing bootstrap support (default 100)"/>
+                <param name="divergence" type="float" value="1.007" label="divergence - Divergence cutoff for chimera determination (default 1.007)"/>
+                <param name="trim" type="boolean" truevalue="true" falsevalue="false" checked="false" label="trim - include chimeric sequences trimmed to their longest peice"/>
+                <param name="split" type="boolean" truevalue="true" falsevalue="false" checked="false" label="split - detect tri- and quadmeras" help="if a sequence comes back as non-chimeric, mothur will test the two sides to see if they are chimeric."/>
+            </when>
+        </conditional>
+        <param name="dereplicate" type="boolean" falsevalue="false" truevalue="true" checked="false" label="dereplicate - remove chimeric sequences from all groups, default=f" help="If parameter is false, then if one group finds the seqeunce to be chimeric, then all groups find it to be chimeric"/>
+    </inputs>
+    <outputs>
+        <expand macro="logfile-output"/>
+        <data name="out_file" from_work_dir="fasta.slayer.chimeras" format="txt" label="${tool.name} on ${on_string}: slayer.chimeras"/>
+        <data name="out_accnos" from_work_dir="fasta.slayer.accnos" format="mothur.accnos" label="${tool.name} on ${on_string}: slayer.accnos"/>
+    </outputs>
+    <tests>
+        <test><!-- test with external reference -->
+            <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head"/>
+            <param name="source" value="hist"/>
+            <param name="template" value="HMP_MOCK.v35.align"/>
+            <output name="out_file" file="Mock_S280_L001_R1_001_small.trim.contigs.good.slayer.chimeras" ftype="txt"/>
+            <expand macro="logfile-test"/>
+        </test>
+        <test><!-- test with self as reference -->
+            <param name="fasta" value="HMP_MOCK.v35.align"/>
+            <param name="source" value="self"/>
+            <param name="setby" value="user"/>
+            <param name="search" value="kmer"/>
+            <param name="name" value="HMP_MOCK.v35.align.names"/>
+            <output name="out_file" file="HMP_MOCK.v35.slayer.chimeras" ftype="txt"/>
+            <expand macro="logfile-test"/>
+        </test>
+    </tests>
+
+    <help>
+<![CDATA[
+
+@MOTHUR_OVERVIEW@
+
+**Command Documentation**
+
+The chimera.slayer_ command identifies putative chimeras using the slayer approach.
+
+ChimeraSlayer_ is a chimeric sequence detection utility, compatible with near-full length Sanger sequences and shorter 454-FLX sequences (~500 bp).
+
+Chimera Slayer involves the following series of steps that operate to flag chimeric 16S rRNA sequences:
+
+    (A) the ends of a query sequence are searched against an included database of reference chimera-free 16S sequences to identify potential parents of a chimera;
+    (B) candidate parents of a chimera are selected as those that form a branched best scoring alignment to the NAST-formatted query sequence;
+    (C) the NAST alignment of the query sequence is improved in a 'chimera-aware' profile-based NAST realignment to the selected reference parent sequences; and
+    (D) an evolutionary framework is used to flag query sequences found to exhibit greater sequence homology to an in silico chimera formed between any two of the selected reference parent sequences.
+
+Note:
+It is not recommended to blindly discard all sequences flagged as chimeras. Some may represent naturally formed chimeras that do not represent PCR artifacts. Sequences flagged may warrant further investigation.
+
+
+.. _ChimeraSlayer: http://microbiomeutil.sourceforge.net/
+.. _chimera.slayer: https://www.mothur.org/wiki/Chimera.slayer
+
+]]>
+    </help>
+    <expand macro="citations"/>
+</tool>