--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pcr.seqs.xml	Fri May 19 05:58:12 2017 -0400
@@ -0,0 +1,159 @@
+<tool profile="16.07" id="mothur_pcr_seqs" name="Pcr.seqs" version="@WRAPPER_VERSION@.0">
+    <description>Trim sequences</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 "$fasta" fasta.dat &&
+        ln -s "$name_in" name_in.dat &&
+        ln -s "$group_in" group_in.dat &&
+        ln -s "$taxonomy_in" taxonomy_in.dat &&
+        #if $trim.method == "oligos":
+            ln -s "$trim.oligos" trim.oligos.dat &&
+        #elif $trim.method == "reference":
+            ln -s "$trim.ecoli" trim.ecoli.dat &&
+        #end if
+
+        echo 'pcr.seqs(
+            fasta=fasta.dat,
+            #if $name_in
+                name=name_in.dat,
+            #end if
+            #if $group_in:
+                group=group_in.dat,
+            #end if
+            #if $taxonomy_in:
+                taxonomy=taxonomy_in.dat,
+            #end if
+            #if $trim.method == "oligos":
+                oligos=trim.oligos.dat,
+                nomatch=$trim.nomatch,
+                $trim.keepprimer
+            #elif $trim.method == "reference":
+                ecoli=trim.ecoli.dat,
+            #elif $trim.method == "position":
+                start=$trim.start,
+                #if $trim.end and int($trim.end) > 0:
+                    end=$trim.end,
+                #end if
+            #end if
+            #if $pdiffs:
+                pdiffs=$pdiffs,
+            #end if
+            $keepdots
+            processors='\${GALAXY_SLOTS:-8}'
+        )'
+        | sed 's/ //g'  ## mothur trips over whitespace
+        | mothur
+        | tee mothur.out.log
+    ]]></command>
+    <inputs>
+        <param name="fasta" type="data" format="mothur.align" label="fasta - Candiate Sequences" help="sequences must be aligned"/>
+        <conditional name="trim">
+            <param name="method" type="select" label="Trim with an oligos file?" help="">
+                <option value="oligos">oligos</option>
+                <option value="reference">reference sequence</option>
+                <option value="position">start and end positions</option>
+            </param>
+            <when value="oligos">
+                <param name="oligos" type="data" format="mothur.oligos" optional="true" label="oligos - barcodes and primers" help="a file that can contain the sequences of the forward and reverse primers and barcodes and their sample identifier. Each line of the oligos file can start with the key words &quot;forward&quot;, &quot;reverse&quot;, and &quot;barcode&quot; or it can start with a &quot;#&quot; to tell mothur to ignore that line of the oligos file."/>
+                <param name="nomatch" type="select" label="nomatch - action when no primer is found">
+                    <option value="reject" selected="true">reject (default)</option>
+                    <option value="keep">keep</option>
+                </param>
+                <param name="keepprimer" type="boolean" falsevalue="" truevalue="keepprimer=true," checked="false" label="keepprimer - keep the primer in the output sequence"/>
+            </when>
+            <when value="reference">
+                <param name="ecoli" type="data" format="mothur.align" optional="true" label="ecoli - An aligned reference sequence for trimming" help="The ecoli parameter is used to provide a fasta file containing a single reference sequence (e.g. for e. coli) this must be aligned. Mothur will trim to the start and end positions of the reference sequence."/>
+            </when>
+            <when value="position">
+                <param name="start" type="integer" min="0" value="0" optional="true" label="start - a starting position to trim to"/>
+                <param name="end" type="integer" value="" optional="true" min="0" label="end - a ending position to trim from"/>
+            </when>
+        </conditional>
+        <param name="keepdots" type="boolean" falsevalue="keepdots=false," truevalue="" checked="true" label="keepdots - keep the leading and trailing alignment dots in the output sequences"/>
+        <param name="taxonomy_in" type="data" format="mothur.seq.taxonomy" optional="true" label="taxonomy - Sequence Taxonomy"/>
+        <param name="name_in" type="data" format="mothur.names" optional="true" label="name - Sequence representative name list"/>
+        <param name="group_in" type="data" format="mothur.groups" optional="true" label="group - Group file"/>
+        <param name="pdiffs" type="integer" value="0" min="0" label="pdiffs - number of differences to allow in the primer (default 0)"/>
+    </inputs>
+    <outputs>
+        <expand macro="logfile-output"/>
+        <data name="pcr_fasta" format="mothur.align" from_work_dir="fasta.pcr.dat" label="${tool.name} on ${on_string}: pcr.fasta"/>
+        <data name="scrap_fasta" format="mothur.align" from_work_dir="fasta.scrap.pcr.dat" label="${tool.name} on ${on_string}: pcr.scrap.fasta"/>
+        <data name="taxonomy_out" format="mothur.seq.taxonomy" from_work_dir="taxonomy_in*.pcr.dat" label="${tool.name} on ${on_string}: tax.summary">
+            <filter>taxonomy_in</filter>
+        </data>
+        <data name="group_out" format="mothur.groups" from_work_dir="group_in*.pcr.dat" label="${tool.name} on ${on_string}: mothur.groups">
+            <filter>group_in</filter>
+        </data>
+        <data name="name_out" format="mothur.names" from_work_dir="name_in*.pcr.dat" label="${tool.name} on ${on_string}: mothur.names">
+            <filter>name_in</filter>
+        </data>
+        <data name="accnos_out" format="mothur.accnos" from_work_dir="fasta*.bad.accnos" label="${tool.name} on ${on_string}: bad.accnos">
+            <filter>trim['method'] =='oligos'</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test><!-- test with position method -->
+            <param name="fasta" value="amazon.align_head" ftype="mothur.align"/>
+            <param name="keepdots" value=""/>
+            <param name="method" value="position"/>
+            <param name="start" value="0"/>
+            <param name="end" value="0"/>
+            <param name="pdiffs" value="0"/>
+            <expand macro="logfile-test"/>
+            <output name="pcr_fasta" md5="4f9c3a835bbba51c64fbf86c8a467d0e" ftype="mothur.align"/>
+            <output name="scrap_fasta" md5="d41d8cd98f00b204e9800998ecf8427e" ftype="mothur.align"/>
+        </test>
+        <test><!-- test with reference method -->
+            <param name="fasta" value="amazon.align_head" ftype="mothur.align"/>
+            <param name="keepdots" value="keepdots=false,"/>
+            <param name="method" value="reference"/>
+            <param name="ecoli" value="amazon.align_head"/>
+            <param name="name_in" value="amazon.align_head.names"/>
+            <param name="pdiffs" value="2"/>
+            <expand macro="logfile-test"/>
+            <output name="pcr_fasta" md5="4bef877bd45f47041f3d17dc017f21ea" ftype="mothur.align"/>
+            <output name="scrap_fasta" md5="d41d8cd98f00b204e9800998ecf8427e" ftype="mothur.align"/>
+            <output name="name_out" md5="0c58174137c2ecabf7da9ab492ea46fc" ftype="mothur.names"/>
+        </test>
+        <test><!-- test with oligos and all outputs -->
+            <param name="fasta" value="amazon.align_head" ftype="mothur.align"/>
+            <param name="method" value="oligos"/>
+            <param name="oligos" value="GQY1XT001.oligos" ftype="mothur.oligos"/>
+            <param name="name_in" value="amazon.names" ftype="mothur.names"/>
+            <param name="group_in" value="amazon.groups" ftype="mothur.groups"/>
+            <param name="taxonomy_in" value="amazon.wang.wang.taxonomy" ftype="mothur.seq.taxonomy"/>
+            <param name="start" value="5"/>
+            <param name="end" value="50"/>
+            <expand macro="logfile-test"/>
+            <output name="pcr_fasta" md5="d41d8cd98f00b204e9800998ecf8427e" ftype="mothur.align"/>
+            <output name="scrap_fasta" md5="0b63807f339dfd88cf958f7b069eba02" ftype="mothur.align"/>
+            <output name="group_out" md5="301c358e61d38c83cc7382a8a210089a" ftype="mothur.groups"/>
+            <output name="name_out" md5="62eb1162557408509c931496071add85" ftype="mothur.names"/>
+            <output name="taxonomy_out" md5="4d72981cefd8b45d4f2793a28dccd9e4" ftype="mothur.seq.taxonomy"/>
+            <output name="accnos_out" md5="48d019b92e4d303faf88a974e52f7a97" ftype="mothur.accnos"/>
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+
+@MOTHUR_OVERVIEW@
+
+**Command Documentation**
+
+The pcr.seqs_ command assigns sequences to chosen taxonomy outline.
+
+.. _pcr.seqs: https://www.mothur.org/wiki/Pcr.seqs
+
+]]>
+    </help>
+    <expand macro="citations"/>
+</tool>