--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/sffinfo.xml	Fri Jun 24 16:40:20 2016 -0400
@@ -0,0 +1,115 @@
+<tool profile="16.07" id="mothur_sffinfo" name="Sffinfo" version="@WRAPPER_VERSION@.0">
+    <description>Summarize the quality of sequences</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="version_command"/>
+    <command detect_errors="aggressive"><![CDATA[
+        ## create symlinks to input datasets
+        ln -s "$sff" sff.dat &&
+        ln -s "$accnos" accnos.dat &&
+        #if $oligo.add == "yes":
+            ln -s "$oligo.oligos" oligo.oligos.dat &&
+        #end if
+
+        echo 'sffinfo(
+            sff=sff.dat,
+            fasta=$fasta,
+            qfile=$qfile,
+            $sfftxt
+            flow=$flow,
+            trim=$trim
+            #if $accnos:
+                ,accnos=accnos.dat
+            #end if
+            #if $oligo.add == "yes":
+                ,oligos=oligo.oligos.dat
+                ,bdiffs=$oligo.bdiffs
+                ,pdiffs=$oligo.pdiffs
+                ,tdiffs=$oligo.tdiffs
+                ,ldiffs=$oligo.ldiffs
+                ,sdiffs=$oligo.sdiffs
+            #end if
+        )'
+        | sed 's/ //g'  ## mothur trips over whitespace
+        | mothur
+    ]]></command>
+    <inputs>
+        <param name="sff" type="data" format="sff" label="sff - Sff data"/>
+        <conditional name="oligo">
+            <param name="add" type="select" label="Trim with an oligos file?" 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.">
+                <option value="no" selected="true">no</option>
+                <option value="yes">yes</option>
+            </param>
+            <when value="no"/>
+            <when value="yes">
+                <param name="oligos" type="data" format="mothur.oligos" label="oligos - barcodes and primers"/>
+                <param name="bdiffs" type="integer" value="0" min="0" label="bdiffs - number of differences to allow in the barcode (default 0)"/>
+                <param name="pdiffs" type="integer" value="0" min="0" label="pdiffs - number of differences to allow in the primer (default 0)"/>
+                <param name="tdiffs" type="integer" value="0" min="0" label="tdiffs - total number of differences to allow in primer and barcode (default 0)"/>
+                <param name="ldiffs" type="integer" value="0" min="0" label="ldiffs - total number of differences to allow in linker sequence (default 0)"/>
+                <param name="sdiffs" type="integer" value="0" min="0" label="sdiffs - total number of differences to allow in spacer sequence (default 0)"/>
+            </when>
+        </conditional>
+        <param name="fasta" type="boolean" truevalue="true" falsevalue="false" checked="true" label="fasta - Add fasta to your history"/>
+        <param name="qfile" type="boolean" truevalue="true" falsevalue="false" checked="true" label="qfile - Add qfile to your history"/>
+        <param name="sfftxt" type="boolean" truevalue="sfftxt=true," falsevalue="" checked="false" label="sfftxt - Add sfftxt to your history"/>
+        <param name="flow" type="boolean" truevalue="true" falsevalue="false" checked="true" label="flow - Add flow to your history"/>
+        <param name="trim" type="boolean" truevalue="true" falsevalue="false" checked="true" label="trim - Trim sequences and quality scores"/>
+        <param name="accnos" type="data" format="mothur.accnos" optional="true" label="accnos - Limit output to named Accessions"/>
+    </inputs>
+    <outputs>
+        <expand macro="logfile-output"/>
+        <data name="out_fasta" format="fasta" from_work_dir="sff*.fasta" label="${tool.name} on ${on_string}: fasta">
+            <filter>fasta</filter>
+        </data>
+        <data name="out_qfile" format="qual454" from_work_dir="sff*.qual" label="${tool.name} on ${on_string}: qual">
+            <filter>qfile</filter>
+        </data>
+        <data name="out_sfftxt" format="txt" from_work_dir="sff*.sff.txt" label="${tool.name} on ${on_string}: sff.txt">
+            <filter>sfftxt</filter>
+        </data>
+        <data name="out_flow" format="mothur.sff.flow" from_work_dir="sff*.flow" label="${tool.name} on ${on_string}: flowgram">
+            <filter>flow</filter>
+        </data>
+        <data name="out_scrap" format="sff" from_work_dir="sff*.scrap.sff" label="${tool.name} on ${on_string}: scrap.sff">
+            <filter>oligo['add'] == 'yes'</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test><!-- test without oligos -->
+            <param name="sff" value="Fasting_Example1.sff"/>
+            <param name="sfftxt" value="true"/>
+            <output name="out_fasta" md5="fbe6f4d51959d4723a8417636476d0e0" ftype="fasta"/>
+            <output name="out_qfile" md5="ffcc4831369139055e1b8e9add9a59c0" ftype="qual454"/>
+            <output name="out_sfftxt" md5="fdc80c8e476016632d317cfd7893713c" ftype="txt"/>
+            <output name="out_flow" md5="34b17477f98ab19c1ff755a61848d968" ftype="mothur.sff.flow"/>
+            <expand macro="logfile-test"/>
+        </test>
+        <test><!-- test with oligos file -->
+            <param name="sff" value="Fasting_Example1.sff"/>
+            <param name="add" value="yes"/>
+            <param name="oligos" value="GQY1XT001.oligos"/>
+            <output name="out_fasta" md5="212fa15e1ed077cecb65ee87f17ef2e1" ftype="fasta"/>
+            <output name="out_qfile" md5="ffcc4831369139055e1b8e9add9a59c0" ftype="qual454"/>
+            <output name="out_flow" md5="34b17477f98ab19c1ff755a61848d968" ftype="mothur.sff.flow"/>
+            <output name="out_scrap" md5="f03c422fe364815e7214ad31ad135aca" ftype="sff"/>
+            <expand macro="logfile-test"/>
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+
+@MOTHUR_OVERVIEW@
+
+**Command Documenation**
+
+The sffinfo_ command will summarize the quality of sequences in an unaligned or aligned fasta-formatted sequence file.
+
+
+.. _sffinfo: http://www.mothur.org/wiki/Sffinfo
+]]>
+    </help>
+    <expand macro="citations"/>
+</tool>