--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/sort.seqs.xml	Fri May 19 05:30:16 2017 -0400
@@ -0,0 +1,132 @@
+<tool profile="16.07" id="mothur_sort_seqs" name="Sort.seqs" version="@WRAPPER_VERSION@.0">
+    <description>put sequences in different files in the same order</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 "$fasta_in" fasta_in.dat &&
+        ln -s "$qfile_in" qfile_in.dat &&
+        ln -s "$flow_in" flow_in.dat &&
+        ln -s "$name_in" name_in.dat &&
+        ln -s "$group_in" group_in.dat &&
+        ln -s "$tax_in" tax_in.dat &&
+        ln -s "$accnos" accnos.dat &&
+        ln -s "$count" count.dat &&
+
+        echo 'sort.seqs(
+            #if $fasta_in:
+                fasta=fasta_in.dat,
+            #end if
+            #if $qfile_in:
+                qfile=qfile_in.dat,
+            #end if
+            #if $flow_in:
+                flow=flow_in.dat,
+            #end if
+            #if $name_in:
+                name=name_in.dat,
+            #end if
+            #if $group_in:
+                group=group_in.dat,
+            #end if
+            #if $tax_in:
+                taxonomy=tax_in.dat,
+            #end if
+            #if $accnos:
+                accnos=accnos.dat,
+            #end if
+            #if $count:
+                count=count.dat,
+            #end if
+            large=$large
+        )'
+        | sed 's/ //g'  ## mothur trips over whitespace
+        | mothur
+        | tee mothur.out.log
+    ]]></command>
+    <inputs>
+        <param name="fasta_in" type="data" format="fasta" optional="true" label="fasta - sequences" help="format must be fasta"/>
+        <param name="qfile_in" type="data" format="qual454" optional="true" label="qfile - sequence quality" help="format must be qual454"/>
+        <param name="flow_in" type="data" format="mothur.sff.flow" optional="true" label="flow - sff flowgram" help="format must be mothur.sff.flow"/>
+        <param name="group_in" type="data" format="mothur.groups" optional="true" label="groups - sequence groupings" help="format must be mothur.groups"/>
+        <param name="name_in" type="data" format="mothur.names" optional="true" label="names - name reference" help="format must be mothur.names"/>
+        <param name="tax_in" type="data" format="mothur.seq.taxonomy" optional="true" label="taxonomy - taxonomy reference" help="format must be mothur.seq.taxonomy"/>
+        <param name="accnos" type="data" format="mothur.accnos" optional="true" label="accnos - sort" help="format must be mothur.accnos"/>
+        <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="format must be mothur.count_table (generated by count.seqs)"/>
+        <param name="large" type="boolean" checked="false" truevalue="true" falsevalue="false" label="large - Datasets are large and may not fit in RAM"/>
+    </inputs>
+    <outputs>
+        <expand macro="logfile-output"/>
+        <data name="fasta_out" format_source="fasta_in" from_work_dir="fasta_in*.sorted.*" label="${tool.name} on ${on_string}: sorted.fasta">
+            <filter>fasta_in</filter>
+        </data>
+        <data name="qfile_out" format_source="qfile_in" from_work_dir="qfile_in*.sorted.*" label="${tool.name} on ${on_string}: sorted.qfile">
+            <filter>qfile_in</filter>
+        </data>
+        <data name="flow_out" format_source="flow_in" from_work_dir="flow_in*.sorted.*" label="${tool.name} on ${on_string}: sorted.flow">
+            <filter>flow_in</filter>
+        </data>
+        <data name="group_out" format_source="group_in" from_work_dir="group_in*.sorted.*" label="${tool.name} on ${on_string}: sorted.group">
+            <filter>group_in</filter>
+        </data>
+        <data name="name_out" format_source="name_in" from_work_dir="name_in*.sorted.*" label="${tool.name} on ${on_string}: sorted.name">
+            <filter>name_in</filter>
+        </data>
+        <data name="taxonomy_out" format_source="tax_in" from_work_dir="tax_in*.sorted.*" label="${tool.name} on ${on_string}: sorted.taxonomy">
+            <filter>tax_in</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="fasta_in" value="amazon.fasta" ftype="fasta"/>
+            <output name="fasta_out" md5="0bc9320647234e8367c3b1b654f9302d" ftype="fasta"/>
+            <expand macro="logfile-test"/>
+        </test>
+        <test>
+            <param name="qfile_in" value="Mock_S280_L001_R1_001_small.trim.contigs.qual" ftype="qual454"/>
+            <output name="qfile_out" md5="abed9d1811786c810a12fd00a376cee4" ftype="qual454"/>
+            <expand macro="logfile-test"/>
+        </test>
+        <test>
+            <param name="group_in" value="amazon.groups" ftype="mothur.groups"/>
+            <output name="group_out" md5="fb60628ae445e7b06f9833f632b2cd0c" ftype="mothur.groups"/>
+            <expand macro="logfile-test"/>
+        </test>
+        <test>
+            <param name="fasta_in" value="amazon.fasta" ftype="fasta"/>
+            <param name="count" value="amazon.count_table" ftype="mothur.count_table"/>
+            <output name="fasta_out" md5="0bc9320647234e8367c3b1b654f9302d" ftype="fasta"/>
+            <expand macro="logfile-test"/>
+        </test>
+        <test><!-- test with multiple file types input -->
+            <param name="fasta_in" value="amazon.fasta" ftype="fasta"/>
+            <param name="qfile_in" value="Mock_S280_L001_R1_001_small.trim.contigs.qual" ftype="qual454"/>
+            <param name="group_in" value="amazon.groups" ftype="mothur.groups"/>
+            <output name="fasta_out" md5="0bc9320647234e8367c3b1b654f9302d" ftype="fasta"/>
+            <output name="qfile_out" md5="abed9d1811786c810a12fd00a376cee4" ftype="qual454"/>
+            <output name="group_out" md5="fb60628ae445e7b06f9833f632b2cd0c" ftype="mothur.groups"/>
+            <expand macro="logfile-test"/>
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+
+@MOTHUR_OVERVIEW@
+
+**Command Documentation**
+
+The sort.seqs_ command puts sequences from a fasta, name, group, quality, flow or taxonomy file in the same order.
+You can provide an accnos file to indicate the order you want, otherwise mothur will use the order of the first file it reads.
+
+.. _sort.seqs: https://www.mothur.org/wiki/Sort.seqs
+
+]]>
+    </help>
+    <expand macro="citations"/>
+</tool>