--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/screen.seqs.xml	Fri Jun 24 16:49:07 2016 -0400
@@ -0,0 +1,158 @@
+<tool profile="16.07" id="mothur_screen_seqs" name="Screen.seqs" version="@WRAPPER_VERSION@.0">
+    <description>Screen 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 "$fasta_in" fasta_in.dat &&
+        ln -s "$names_in" names_in.dat &&
+        ln -s "$groups_in" groups_in.dat &&
+        ln -s "$qfile_in" qfile_in.dat &&
+        ln -s "$count_in" count_in.dat &&
+        ln -s "$alignreport_in" alignreport_in.dat &&
+        ln -s "$taxonomy_in" taxonomy_in.dat &&
+        ln -s "$summary" summary.dat &&
+        ln -s "$contigsreport" contigsreport.dat &&
+
+        echo 'screen.seqs(
+            fasta=fasta_in.dat
+            #if $start > -1:
+                ,start=$start
+            #end if
+            #if $end > -1:
+                ,end=$end
+            #end if
+            #if $minlength > -1:
+                ,minlength=$minlength
+            #end if
+            #if $maxlength > -1:
+                ,maxlength=$maxlength
+            #end if
+            #if $maxambig > -1:
+                ,maxambig=$maxambig
+            #end if
+            #if $maxhomop > -1:
+                ,maxhomop=$maxhomop
+            #end if
+            #if $criteria > -1:
+                ,criteria=$criteria
+            #end if
+            #if $optimize:
+                ,optimize=$optimize
+            #end if
+            #if $qfile_in:
+                ,qfile=qfile_in.dat
+            #end if
+            #if $names_in:
+                ,name=names_in.dat
+            #end if
+            #if $groups_in:
+                ,group=groups_in.dat
+            #end if
+            #if $alignreport_in:
+                ,alignreport=alignreport_in.dat
+            #end if
+            #if $taxonomy_in:
+                ,taxonomy=taxonomy_in.dat
+            #end if
+            #if $count_in:
+                ,count=count_in.dat
+            #end if
+            #if $summary:
+                ,summary=summary.dat
+            #end if
+            #if $contigsreport:
+                ,contigsreport=contigsreport.dat
+            #end if
+            ,processors='"\${GALAXY_SLOTS:-8}"'
+        )'
+        | sed 's/ //g'  ## mothur trips over whitespace
+        | mothur
+    ]]></command>
+    <inputs>
+        <param name="fasta_in" type="data" format="fasta,mothur.align" label="fasta - Fasta to screen"/>
+        <param name="start" type="integer" value="-1" label="start - Remove sequences that start after position (ignored when negative)"/>
+        <param name="end" type="integer" value="-1" label="end - Remove sequences that end before position (ignored when negative)"/>
+        <param name="minlength" type="integer" value="-1" label="minlength - Remove sequences shorter than (ignored when negative)"/>
+        <param name="maxlength" type="integer" value="-1" label="maxlength - Remove sequences longer than (ignored when negative)"/>
+        <param name="maxambig" type="integer" value="-1" label="maxambig - Remove sequences with ambiguous bases greater than (ignored when negative)"/>
+        <param name="maxhomop" type="integer" value="-1" label="maxhomop - Remove sequences with homopolymers greater than (ignored when negative)"/>
+        <param name="criteria" type="integer" value="-1" label="criteria - Percent of sequences that an optimize value must match to be retained(ignored when negative)"/>
+        <param name="optimize" type="select" multiple="true" display="checkboxes" label="optimize - Optimize selected paramenters">
+            <option value="start">start</option>
+            <option value="end">end</option>
+            <option value="minlength">minlength</option>
+            <option value="maxlength">maxlength</option>
+            <option value="maxambig">maxambig</option>
+            <option value="maxhomop">maxhomop</option>
+        </param>
+        <param name="qfile_in" type="data" format="qual" optional="true" label="qfile - Sequence Quality file to screen"/>
+        <param name="names_in" type="data" format="mothur.names" optional="true" label="name - Sequence Names to screen"/>
+        <param name="groups_in" type="data" format="mothur.groups" optional="true" label="group - Groups to screen"/>
+        <param name="alignreport_in" type="data" format="mothur.align.report" optional="true" label="alignreport - Align Report to screen"/>
+        <param name="summary" type="data" format="mothur.summary" optional="true" label="summary - allows you to enter the summary file created by summary.seqs to save processing time when screening with parameters in the summary file"/>
+        <param name="contigsreport" type="data" format="contigs.report" optional="true" label="contigsreport - Contigs Report to screen with" help="this file is created by the make.contigs command. If you provide the contigs report file you can screen your sequences using the following parameters: minoverlap, ostart, oend and mismatches"/>
+        <param name="taxonomy_in" type="data" format="taxonomy" optional="true" label="taxonomy - Taxonomy to screen"/>
+        <param name="count_in" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/>
+    </inputs>
+    <outputs>
+        <expand macro="logfile-output"/>
+        <data name="fasta_out" format_source="fasta_in" from_work_dir="fasta_in*.good.dat" label="${tool.name} on ${on_string}: good.${fasta_in.datatype.file_ext}"/>
+        <data name="bad_accnos" format="mothur.accnos" from_work_dir="fasta_in*.bad.accnos" label="${tool.name} on ${on_string}: bad.accnos"/>
+        <data name="qfile_out" format_source="qfile_in" from_work_dir="qfile_in*.good.dat" label="${tool.name} on ${on_string}: qfile">
+            <filter>qfile_in</filter>
+        </data>
+        <data name="names_out" format="mothur.names" from_work_dir="names_in*.good.dat" label="${tool.name} on ${on_string}: names">
+            <filter>names_in</filter>
+        </data>
+        <data name="groups_out" format="mothur.groups" from_work_dir="groups_in*.good.dat" label="${tool.name} on ${on_string}: groups">
+            <filter>groups_in</filter>
+        </data>
+        <data name="alignreport_out" format="mothur.align.report" from_work_dir="alignreport_in*.good.dat" label="${tool.name} on ${on_string}: align.report">
+            <filter>alignreport_in</filter>
+        </data>
+        <data name="count_out" format="count" from_work_dir="count_in*.good.dat" label="${tool.name} on ${on_string}: count">
+            <filter>count_in</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="fasta_in" value="Mock_S280_L001_R1_001_small.trim.contigs.fasta"/>
+            <param name="maxambig" value="0"/>
+            <param name="maxlength" value="275"/>
+            <output name="fasta_out" file="Mock_S280_L001_R1_001_small.trim.contigs.good.fasta"/>
+            <output name="bad_accnos" file="Mock_S280_L001_R1_001_small.trim.contigs.bad.accnos"/>
+            <expand macro="logfile-test"/>
+        </test>
+        <test>
+            <param name="fasta_in" value="amazon.fasta"/>
+            <param name="count_in" value="amazon.count_table"/>
+            <param name="maxambig" value="0"/>
+            <param name="maxlength" value="275"/>
+            <output name="fasta_out" md5="d41d8cd98f00b204e9800998ecf8427e"/>
+            <output name="count_out" md5="5f4a08bbf3ec12f954edbcc6b2a2feee"/>
+            <output name="bad_accnos" md5="66acde5349e34fc97be22032ce68eea5"/>
+            <expand macro="logfile-test"/>
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+
+@MOTHUR_OVERVIEW@
+
+**Command Documenation**
+
+The screen.seqs_ command enables you to keep sequences that fulfill certain user defined criteria. Furthermore, it enables you to cull those sequences not meeting the criteria from a name_, group_, or align.report_ file.
+
+.. _name: http://www.mothur.org/wiki/Name_file
+.. _group: http://www.mothur.org/wiki/Group_file
+.. _align.report: http://www.mothur.org/wiki/Align.seqs
+.. _screen.seqs: http://www.mothur.org/wiki/Screen.seqs
+
+]]>
+    </help>
+    <expand macro="citations"/>
+</tool>