--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/chimera.uchime.xml	Fri May 19 05:50:35 2017 -0400
@@ -0,0 +1,177 @@
+<tool profile="16.07" id="mothur_chimera_uchime" name="Chimera.uchime" version="@WRAPPER_VERSION@.0">
+    <description>Find putative chimeras using uchime</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <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.uchime(
+            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=$dn,
+            xa=$xa,
+            chunks=$chunks,
+            minchunk=$minchunk,
+            #if $idsmoothwindow:
+                idsmoothwindow=$idsmoothwindow,
+            #end if
+            maxp=$maxp,
+            minlen=$minlen,
+            maxlen=$maxlen,
+            skipgaps=$skipgaps,
+            skipgaps2=$skipgaps2,
+            #if $alignment.ucl == "local":
+                ucl=true,
+                #if $alignment.queryfract:
+                    queryfract=$alignment.queryfract,
+                #end if
+            #end if
+            dereplicate=$dereplicate,
+            chimealns=$chimealns,
+            processors='\${GALAXY_SLOTS:-8}'
+        )'
+        | sed 's/ //g'  ## mothur trips over whitespace
+        | mothur
+        | tee mothur.out.log
+        2>&1  ## uchime component writes output to stderr
+    ]]></command>
+    <inputs>
+        <param name="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" help="">
+                <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 name="reference" type="select" label="reference - Select an alignment database " help="">
+                    <options from_data_table="mothur_aligndb">
+                    </options>
+                </param>
+            </when>
+            <when value="hist">
+                <param name="reference" type="data" format="fasta" label="reference - Reference to align with" help=""/>
+            </when>
+            <when value="self">
+                <param name="abskew" type="float" value="1.9" label="abskew - Abundance skew (default 1.9)" help="Abundance skew is: min [ abund(parent1), abund(parent2) ] / abund(query)"/>
+                <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"/>
+                <param name="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 *.pick.count_table file containing seqeunces after chimeras are removed."/>
+            </when>
+            <when value="names">
+                <param name="name" type="data" format="mothur.names" label="name - Sequence names"/>
+            </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"/>
+        <param name="skipgaps" type="boolean" falsevalue="false" truevalue="true" checked="true" label="skipgaps - columns containing gaps do not count as diffs. Default=T" help="controls how gapped columns affect counting of diffs"/>
+        <param name="skipgaps2" type="boolean" falsevalue="false" truevalue="true" checked="true" label="skipgaps2 - column is immediately adjacent to a column containing a gap, it is not counted as a diff. Default=T" help="controls how gapped columns affect counting of diffs"/>
+        <param name="chimealns" type="boolean" falsevalue="false" truevalue="true" checked="false" label="chimealns - Produce a file containing multiple alignments of query sequences to parents in human readable format. " help="Alignments show columns with differences that support or contradict a chimeric model."/>
+        <param name="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 name="mindiv" type="float" value="0.5" min="0" label="mindiv - minimum divergence ratio, default 0.5" help="to ignore very close chimeras, increase mindiv to 1.0 or 2.0, to increase sensitivity decrease minh to 0.1"/>
+        <param name="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 name="dn" type="float" value="1.4" min="0" label="dn - pseudo-count prior on number of no votes. Default 1.4" help="Reasonable values are probably in the range from 0.2 to 2.0"/>
+        <param name="xa" type="float" value="1.0" min="0" label="xa - eight of an abstain vote. Default 1.0" help="Reasonable values might range from 0.1 to 2.0"/>
+        <param name="chunks" type="integer" value="4" min="0" label="chunks - number of chunks. Default 4." help="number of chunks to extract from the query sequence when searching for parents."/>
+        <param name="minchunk" type="integer" value="64" min="0" label="minchunk - minimum length of a chunk. Default 64." help=""/>
+        <param name="maxp" type="integer" value="2" min="0" label="maxp - maximum number of candidate parents to consider. Default 2" help="increasing maxp gives only a very small improvement in sensivity but tends to increase the error rate quite a bit"/>
+        <param name="minlen" type="integer" value="10" min="0" label="minlen - minimum unaligned sequence length. Default 10" help="Applies to both query and reference sequences."/>
+        <param name="maxlen" type="integer" value="10000" min="0" label="maxlen - maximum unaligned sequence length. Defaults 10000" help="Applies to both query and reference sequences."/>
+        <param name="idsmoothwindow" type="integer" value="32" min="0" optional="True" label="idsmoothwindow - the length of id smoothing window. Default 32" help=""/>
+        <conditional name="alignment">
+            <param name="ucl" type="select" label="ucl - Use local-X alignments" help="global-X is the default">
+                <option value="global" selected="true">global</option>
+                <option value="local">local</option>
+            </param>
+            <when value="global"/>
+            <when value="local">
+                <param name="queryfract" type="float" value="0.5" min="0" max="1" label="queryfract - minimum fraction of the query sequence that must be covered by a local-X alignment. Default 0.5." help=""/>
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <expand macro="logfile-output"/>
+        <data name="out_file" format="txt" from_work_dir="fasta.*uchime.chimeras" label="${tool.name} on ${on_string}: uchime.chimeras"/>
+        <data name="out_accnos" format="mothur.accnos" from_work_dir="fasta.*uchime.accnos" label="${tool.name} on ${on_string}: uchime.accnos"/>
+        <data name="out_alns" format="txt" from_work_dir="fasta.*uchime.alns" label="${tool.name} on ${on_string}: uchime.alns">
+            <filter>chimealns</filter>
+        </data>
+        <data name="out_count" format="mothur.count_table" from_work_dir="template.*uchime.pick.count_table" label="${tool.name} on ${on_string}: uchime.count_table">
+            <filter>template['count']</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test><!-- default params test -->
+            <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head_withchimera"/>
+            <param name="source" value="hist"/>
+            <param name="reference" value="HMP_MOCK.v35.align"/>
+            <output name="out_file" file="Mock_S280_L001_R1_001_small.trim.contigs.good.ref.uchime.chimeras" ftype="txt"/>
+            <output name="out_accnos" file="Mock_S280_L001_R1_001_small.trim.contigs.good.ref.uchime.accnos" ftype="mothur.accnos"/>
+            <expand macro="logfile-test"/>
+        </test>
+        <test><!-- de novo test -->
+            <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head"/>
+            <param name="source" value="self"/>
+            <output name="out_file" file="Mock_S280_L001_R1_001_small.trim.contigs.good.denovo.uchime.chimeras" ftype="txt"/>
+            <output name="out_accnos" md5="d41d8cd98f00b204e9800998ecf8427e" ftype="mothur.accnos"/>
+            <expand macro="logfile-test"/>
+        </test>
+        <test><!-- with chimealns output -->
+            <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head_withchimera"/>
+            <param name="source" value="hist"/>
+            <param name="reference" value="HMP_MOCK.v35.align"/>
+            <param name="chimealns" value="true"/>
+            <output name="out_file" file="Mock_S280_L001_R1_001_small.trim.contigs.good.ref.uchime.chimeras" ftype="txt"/>
+            <output name="out_accnos" file="Mock_S280_L001_R1_001_small.trim.contigs.good.ref.uchime.accnos" ftype="mothur.accnos"/>
+            <output name="out_alns" file="Mock_S280_L001_R1_001_small.trim.contigs.good.ref.uchime.alns" ftype="txt"/>
+            <expand macro="logfile-test"/>
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+
+@MOTHUR_OVERVIEW@
+
+**Command Documentation**
+
+The chimera.uchime_ command reads a fasta file and reference file and outputs potentially chimeric sequences. The original uchime program was written by Robert C. Edgar and donated to the public domain, http://drive5.com/uchime
+
+.. _chimera.uchime: https://www.mothur.org/wiki/Chimera.uchime
+
+Version 1.23.0: Upgrades tool dependency to mothur 1.33 and adds support for count (mothur 1.28) and dereplicate (mothur 1.29) options.
+]]>
+    </help>
+    <expand macro="citations"/>
+</tool>