--- a/chimera.uchime.xml	Tue Sep 05 17:00:36 2017 -0400
+++ b/chimera.uchime.xml	Tue Mar 20 22:21:36 2018 -0400
@@ -7,129 +7,151 @@
     <expand macro="stdio"/>
     <expand macro="version_command"/>
     <command><![CDATA[
-        @SHELL_OPTIONS@
+@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 "$template.reference" template.reference.dat &&
-        #end if
+## create symlinks to input datasets
+ln -s '$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
+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"/>
+        <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" help="">
+            <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 name="reference" type="select" label="reference - Select an alignment database " help="">
-                    <options from_data_table="mothur_aligndb">
-                    </options>
+                <param argument="reference" type="select" label="reference - Select an alignment database">
+                    <options from_data_table="mothur_aligndb"/>
                 </param>
             </when>
             <when value="hist">
-                <param name="reference" type="data" format="fasta" label="reference - Reference to align with" help=""/>
+                <param argument="reference" type="data" format="fasta" label="reference - Reference to align with"/>
             </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."/>
+                <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 name="name" type="data" format="mothur.names" label="name - Sequence names"/>
+                <param argument="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=""/>
+        <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="skipgaps" type="boolean" falsevalue="false" truevalue="true" checked="true"
+            label="skipgaps - columns containing gaps do not count as diffs"
+            help="controls how gapped columns affect counting of diffs"/>
+        <param argument="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"
+            help="controls how gapped columns affect counting of diffs"/>
+        <param argument="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 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="xa" type="float" value="1.0" min="0" label="xa - eight of an abstain vote"
+            help="Reasonable values might range from 0.1 to 2.0. Default 1.0"/>
+        <param argument="chunks" type="integer" value="4" min="0" label="chunks - number of chunks"
+            help="number of chunks to extract from the query sequence when searching for parents.  Default 4."/>
+        <param argument="minchunk" type="integer" value="64" min="0" label="minchunk - minimum length of a chunk" help="Default 64"/>
+        <param argument="maxp" type="integer" value="2" min="0" label="maxp - maximum number of candidate parents to consider"
+            help="increasing maxp gives only a very small improvement in sensivity but tends to increase the error rate quite a bit. Default 2"/>
+        <param argument="minlen" type="integer" value="10" min="0" label="minlen - minimum unaligned sequence length"
+            help="Applies to both query and reference sequences. Default 10"/>
+        <param argument="maxlen" type="integer" value="10000" min="0" label="maxlen - maximum unaligned sequence length"
+            help="Applies to both query and reference sequences. Default 10000"/>
+        <param argument="idsmoothwindow" type="integer" value="32" min="0" optional="True" label="idsmoothwindow - the length of id smoothing window"
+            help="Default 32"/>
         <conditional name="alignment">
-            <param name="ucl" type="select" label="ucl - Use local-X alignments" help="global-X is the default">
+            <param argument="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=""/>
+                <param argument="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" help="Default 0.5"/>
             </when>
         </conditional>
+        <expand macro="param-savelog"/>
     </inputs>
     <outputs>
         <expand macro="logfile-output"/>
-        <data name="out_file" format="txt" from_work_dir="fasta.*uchime.chimeras" label="${tool.name} on ${on_string}: uchime.chimeras"/>
+        <data name="uchime.chimeras" format="txt" from_work_dir="fasta.*uchime.chimeras" label="${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>
+            <filter>template['source'] == 'self' and template['count']</filter>
         </data>
     </outputs>
     <tests>
@@ -137,15 +159,17 @@
             <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="uchime.chimeras" 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"/>
+            <param name="savelog" value="true"/>
             <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="uchime.chimeras" file="Mock_S280_L001_R1_001_small.trim.contigs.good.denovo.uchime.chimeras" ftype="txt"/>
             <output name="out_accnos" md5="d41d8cd98f00b204e9800998ecf8427e" ftype="mothur.accnos"/>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
         <test><!-- with chimealns output -->
@@ -153,14 +177,14 @@
             <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="uchime.chimeras" 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"/>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 
 @MOTHUR_OVERVIEW@
 
@@ -171,7 +195,7 @@
 .. _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>
+
+    ]]></help>
     <expand macro="citations"/>
 </tool>