--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rename.seqs.xml	Tue Mar 20 22:01:03 2018 -0400
@@ -0,0 +1,111 @@
+<tool profile="16.07" id="mothur_rename_seqs" name="Rename.seqs" version="@WRAPPER_VERSION@.0">
+    <description>Rename sequences by concatenating the group name</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 '$fasta' fasta.dat &&
+ln -s '$group' group.dat &&
+ln -s '$name' name.dat &&
+ln -s '$qfile' qfile.dat &&
+ln -s '$contigsreport' contigsreport.dat &&
+
+echo 'rename.seqs(
+    fasta=fasta.dat,
+    group=group.dat,
+    #if $name:
+        name=name.dat,
+    #end if
+    #if $qfile:
+        qfile=qfile.dat,
+    #end if
+    #if $contigsreport:
+        contigsreport=contigsreport.dat,
+    #end if
+    placement=$placement
+)'
+| sed 's/ //g'  ## mothur trips over whitespace
+| mothur
+| tee mothur.out.log
+    ]]></command>
+    <inputs>
+        <param argument="fasta" type="data" format="fasta,mothur.align" label="Fasta file"/>
+        <param argument="group" type="data" format="mothur.groups" label="Group file"/>
+        <param argument="name" type="data" format="mothur.names" optional="true" label="Names file"/>
+        <param argument="qfile" type="data" format="qual454" optional="true" label="quality file"/>
+        <param argument="contigsreport" type="data" format="tabular" optional="true" label="Contigsreport file"/>
+        <param argument="placement" type="select" label="Placement of group name">
+            <option value="back" selected="true">back</option>
+            <option value="front">front</option>
+        </param>
+        <expand macro="param-savelog"/>
+    </inputs>
+    <outputs>
+        <expand macro="logfile-output"/>
+        <data name="group_renamed" format="mothur.groups" from_work_dir="group.renamed.dat" label="${tool.name} on ${on_string}: group_renamed"/>
+        <data name="fasta_renamed" format_source="fasta" from_work_dir="fasta.renamed.dat" label="${tool.name} on ${on_string}: fasta_renamed"/>
+        <data name="map" format="tabular" from_work_dir="fasta.renamed_map" label="${tool.name} on ${on_string}: renaming map"/>
+        <data name="name_renamed" format="mothur.names" from_work_dir="name.renamed.dat" label="${tool.name} on ${on_string}: name_renamed">
+            <filter>name</filter>
+        </data>
+        <data name="qfile_renamed" format="qual454" from_work_dir="qfile.renamed.dat" label="${tool.name} on ${on_string}: qfile_renamed">
+            <filter>qfile</filter>
+        </data>
+        <data name="contigsreport_renamed" format="tabular" from_work_dir="contigsreport.renamed.dat" label="${tool.name} on ${on_string}: contigsreport_renamed">
+            <filter>contigsreport</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test><!-- test with required params -->
+            <param name="fasta" value="amazon.fasta" ftype="fasta"/>
+            <param name="group" value="amazon.groups"/>
+            <param name="name" value="amazon1.names"/>
+            <output name="fasta_renamed" ftype="fasta">
+                <assert_contents>
+                    <expand macro="test-fasta-format"/>
+                    <has_text text="42_forest"/>
+                    <has_text text="42_pasture"/>
+                </assert_contents>
+            </output>
+            <output name="map" ftype="tabular">
+                <assert_contents>
+                    <has_n_columns n="2"/>
+                    <has_line_matching expression="^42_forest\tU68631$"/>
+                </assert_contents>
+            </output>
+            <output name="group_renamed" ftype="mothur.groups">
+                <assert_contents>
+                    <has_n_columns n="2"/>
+                    <has_line_matching expression="^42_forest\tforest$"/>
+                </assert_contents>
+            </output>
+            <output name="name_renamed" ftype="mothur.names">
+                <assert_contents>
+                    <has_n_columns n="2"/>
+                    <has_line_matching expression="^42_forest\t42_forest$"/>
+                </assert_contents>
+            </output>
+            <param name="savelog" value="true"/>
+            <expand macro="logfile-test"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+@MOTHUR_OVERVIEW@
+
+**Command Documentation**
+
+The rename.seqs_ command takes fasta-formatted sequence file and group file, and renames
+the sequences by appending the group name to the sequence number.
+
+.. _rename.seqs: https://www.mothur.org/wiki/Rename.seqs
+
+    ]]></help>
+    <expand macro="citations"/>
+</tool>