--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/seq.error.xml	Fri May 19 05:42:13 2017 -0400
@@ -0,0 +1,172 @@
+<tool profile="16.07" id="mothur_seq_error" name="Seq.error" version="@WRAPPER_VERSION@.0">
+    <description>assess error rates in sequencing data</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 "$fasta_in" fasta_in.dat &&
+        ln -s "$name_in" name_in.dat &&
+        ln -s "$count" count.dat &&
+        ln -s "$alignment.template" alignment.template.dat &&
+        #if $qual.use == "yes":
+            ln -s "$qual.qfile_in" qfile_in.dat &&
+            ln -s "$qual.alignreport_in" alignreport_in.dat &&
+        #end if
+
+        echo 'seq.error(
+            fasta=fasta_in.dat,
+            reference=alignment.template.dat,
+            #if $name_in:
+                name=name_in.dat,
+            #end if
+            #if $qual.use == "yes":
+                qfile=qfile_in.dat,
+                report=alignreport_in.dat,
+            #end if
+            #if $threshold:
+                threshold=$threshold,
+            #end if
+            ignorechimeras=$ignorechimeras,
+            #if $count:
+                count=count.dat,
+            #end if
+            #if $fasta_in.is_of_type('mothur.align')
+                aligned=T,
+            #else
+                aligned=F,
+            #end if
+            processors='\${GALAXY_SLOTS:-8}'
+        )'
+        | sed 's/ //g'  ## mothur trips over whitespace
+        | mothur
+        | tee mothur.out.log
+    ]]></command>
+    <inputs>
+        <param name="fasta_in" type="data" format="mothur.align,fasta" label="fasta - Candidate Sequences" help="sequences must be aligned"/>
+        <conditional name="alignment">
+            <param name="source" type="select" label="Select Reference Template from" help="">
+                <option value="ref">Cached Reference</option>
+                <option value="history">Your History</option>
+            </param>
+            <when value="ref">
+                <param name="template" type="select" label="reference - Select an alignment database" help="">
+                    <options from_data_table="mothur_aligndb"/>
+                </param>
+            </when>
+            <when value="history">
+                <param name="template" type="data" format="mothur.align,fasta" label="reference - Reference to align with" help=""/>
+            </when>
+        </conditional>
+        <param name="name_in" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference"/>
+        <conditional name="qual">
+            <param name="use" type="select" label="Include a quality file and an alignment report as inputs" help="">
+                <option value="no">No</option>
+                <option value="yes">Yes</option>
+            </param>
+            <when value="yes">
+                <param name="qfile_in" type="data" format="qual" label="qfile - Fasta Quality"/>
+                <param name="alignreport_in" type="data" format="mothur.align.report" label="alignreport - Align Report"/>
+            </when>
+            <when value="no"/>
+        </conditional>
+        <param name="count" type="data" format="mothur.count_table" optional="true" label="count table"/>
+        <param name="threshold" type="float" value="" min="0" max="1" optional="true" label="threshold - error rate at which to report (default 1.)"/>
+        <param name="ignorechimeras" type="boolean" truevalue="true" falsevalue="false" checked="true" label="ignorechimeras - "/>
+    </inputs>
+    <outputs>
+        <expand macro="logfile-output"/>
+        <data name="summary_out" format="tabular" from_work_dir="fasta_in*.error.summary" label="${tool.name} on ${on_string}: error.summary">
+            <filter>'summary' in output_sel</filter>
+        </data>
+        <data name="seq_out" format="fasta" from_work_dir="fasta_in*.error.seq" label="${tool.name} on ${on_string}: error.seq">
+            <filter>'seq' in output_sel</filter>
+        </data>
+        <data name="seq_forward_out" format="tabular" from_work_dir="fasta_in*.error.seq.forward" label="${tool.name} on ${on_string}: error.seq.forward">
+            <filter>'seq_forward' in output_sel</filter>
+        </data>
+        <data name="seq_reverse_out" format="tabular" from_work_dir="fasta_in*.error.seq.reverse" label="${tool.name} on ${on_string}: error.seq.reverse">
+            <filter>'seq_reverse' in output_sel</filter>
+        </data>
+        <data name="chimera_out" format="tabular" from_work_dir="fasta_in*.error.chimera" label="${tool.name} on ${on_string}: error.chimera">
+            <filter>'chimera' in output_sel</filter>
+        </data>
+        <data name="count_out" format="tabular" from_work_dir="fasta_in*.error.count" label="${tool.name} on ${on_string}: error.count">
+            <filter>'count' in output_sel</filter>
+        </data>
+        <data name="matrix_out" format="tabular" from_work_dir="fasta_in*.error.matrix" label="${tool.name} on ${on_string}: error.matrix">
+            <filter>'matrix' in output_sel</filter>
+        </data>
+        <data name="quality_out" format="tabular" from_work_dir="fasta_in*.error.quality" label="${tool.name} on ${on_string}: error.quality">
+            <filter>qual['use'] == 'yes' and 'quality' in output_sel</filter>
+        </data>
+        <data name="qual_forward_out" format="tabular" from_work_dir="fasta_in*.error.qual.forward" label="${tool.name} on ${on_string}: error.qual.forward">
+            <filter>qual['use'] == 'yes' and 'qual_forward' in output_sel</filter>
+        </data>
+        <data name="qual_reverse_out" format="tabular" from_work_dir="fasta_in*.error.qual.reverse" label="${tool.name} on ${on_string}: error.qual.reverse">
+            <filter>qual['use'] == 'yes' and 'qual_reverse' in output_sel</filter>
+        </data>
+        <data name="ref_query_out" format="mothur.align" from_work_dir="fasta_in*.error.ref" label="${tool.name} on ${on_string}: error.ref-query">
+            <filter>'ref_query' in output_sel</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test><!--test with all outputs and no qual file-->
+            <param name="fasta_in" value="amazon.align_head" ftype="mothur.align"/>
+            <param name="template" value="HMP_MOCK.v35.align" ftype="mothur.align"/>
+            <param name="source" value="history"/>
+            <param name="output_sel" value="summary,seq,seq_forward,seq_reverse,chimera,count,matrix,ref_query"/>
+            <output name="chimera_out" md5="9faf0da7d724a1db5e0d8f5fcb72b486"/>
+            <output name="count_out" md5="9aea787346ad6a1c496aa1d77262a487"/>
+            <output name="matrix_out" md5="b7d9bbf3cdf363b41551e31c0b460a47"/>
+            <output name="ref_query_out" md5="42b42eb4c6bc2705ded2c697a757106f"/>
+            <output name="seq_out" md5="5a884846a8d94b8482c2935d2e7e43e6"/>
+            <output name="seq_forward_out" md5="92a24ef3155bc050ae4fd31bab43cf92"/>
+            <output name="seq_reverse_out" md5="92a24ef3155bc050ae4fd31bab43cf92"/>
+            <output name="summary_out" md5="04abbbd6aa82f084e4a3bd51c4ce98e6"/>
+            <expand macro="logfile-test"/>
+        </test>
+        <test><!--test with qual file and all outputs -->
+            <param name="fasta_in" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head" ftype="mothur.align"/>
+            <param name="template" value="HMP_MOCK.v35.align" ftype="mothur.align"/>
+            <param name="source" value="history"/>
+            <param name="output_sel" value="summary,seq,seq_forward,seq_reverse,chimera,count,matrix,ref_query,quality,qual_forward,qual_reverse"/>
+            <param name="use" value="yes"/>
+            <param name="qfile_in" value="Mock_S280_L001_R1_001_small.trim.contigs.qual"/>
+            <param name="alignreport_in" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align.report"/>
+            <output name="chimera_out" md5="78e586f1a1362fd98808d7725d786caa"/>
+            <output name="count_out" md5="ee987c7b5dc90d4d3a0ef55d817cc540"/>
+            <output name="matrix_out" md5="6b9310b4acd95c560cd062b620b35826"/>
+            <output name="ref_query_out" md5="dd569264c5a4628079de3ef828766e90"/>
+            <output name="quality_out" md5="844b50d6642381a7f434b8182b9307da"/>
+            <output name="qual_forward_out" md5="371fc760fc51b5adf10044fc26c1bbb8"/>
+            <output name="qual_reverse_out" md5="81f17617ba99cac5807e454a626eb006"/>
+            <output name="seq_out" md5="69a8ec131df0b1d4d95eaeb04e057941"/>
+            <output name="seq_forward_out" md5="dbcbbefdc83c2a7c045e3930850cdbd9"/>
+            <output name="seq_reverse_out" md5="5618b1e431306ec1275f1572d6c0c2fc"/>
+            <output name="summary_out" md5="d33bddf9b112f2f3a80b38cf7ac50e6a"/>
+            <expand macro="logfile-test"/>
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+
+@MOTHUR_OVERVIEW@
+
+**Command Documentation**
+
+The seq.error_ command evaluates error rate for sequences by comparing to the fasta-formatted template_alignment_.
+This is demonstrated in https://www.mothur.org/wiki/Schloss_SOP#Error_analysis
+
+.. _template_alignment: https://www.mothur.org/wiki/Alignment_database
+.. _seq.error: https://www.mothur.org/wiki/Seq.error
+
+]]>
+    </help>
+    <expand macro="citations"/>
+</tool>