--- a/screen.seqs.xml	Fri Jun 24 16:49:07 2016 -0400
+++ b/screen.seqs.xml	Fri May 19 05:17:26 2017 -0400
@@ -4,8 +4,11 @@
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements"/>
+    <expand macro="stdio"/>
     <expand macro="version_command"/>
-    <command detect_errors="aggressive"><![CDATA[
+    <command><![CDATA[
+        @SHELL_OPTIONS@
+
         ## create symlinks to input datasets
         ln -s "$fasta_in" fasta_in.dat &&
         ln -s "$names_in" names_in.dat &&
@@ -19,25 +22,25 @@
 
         echo 'screen.seqs(
             fasta=fasta_in.dat
-            #if $start > -1:
+            #if int($start) > -1:
                 ,start=$start
             #end if
-            #if $end > -1:
+            #if int($end) > -1:
                 ,end=$end
             #end if
-            #if $minlength > -1:
+            #if int($minlength) > -1:
                 ,minlength=$minlength
             #end if
-            #if $maxlength > -1:
+            #if int($maxlength) > -1:
                 ,maxlength=$maxlength
             #end if
-            #if $maxambig > -1:
+            #if int($maxambig) > -1:
                 ,maxambig=$maxambig
             #end if
-            #if $maxhomop > -1:
+            #if int($maxhomop) > -1:
                 ,maxhomop=$maxhomop
             #end if
-            #if $criteria > -1:
+            #if int($criteria) > -1:
                 ,criteria=$criteria
             #end if
             #if $optimize:
@@ -71,6 +74,7 @@
         )'
         | sed 's/ //g'  ## mothur trips over whitespace
         | mothur
+        | tee mothur.out.log
     ]]></command>
     <inputs>
         <param name="fasta_in" type="data" format="fasta,mothur.align" label="fasta - Fasta to screen"/>
@@ -93,7 +97,7 @@
         <param name="names_in" type="data" format="mothur.names" optional="true" label="name - Sequence Names to screen"/>
         <param name="groups_in" type="data" format="mothur.groups" optional="true" label="group - Groups to screen"/>
         <param name="alignreport_in" type="data" format="mothur.align.report" optional="true" label="alignreport - Align Report to screen"/>
-        <param name="summary" type="data" format="mothur.summary" optional="true" label="summary - allows you to enter the summary file created by summary.seqs to save processing time when screening with parameters in the summary file"/>
+        <param name="summary" type="data" format="mothur.summary" optional="true" label="summary file - as created by summary.seqs" help="saves processing time when screening with parameters in the summary file"/>
         <param name="contigsreport" type="data" format="contigs.report" optional="true" label="contigsreport - Contigs Report to screen with" help="this file is created by the make.contigs command. If you provide the contigs report file you can screen your sequences using the following parameters: minoverlap, ostart, oend and mismatches"/>
         <param name="taxonomy_in" type="data" format="taxonomy" optional="true" label="taxonomy - Taxonomy to screen"/>
         <param name="count_in" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/>
@@ -114,27 +118,27 @@
         <data name="alignreport_out" format="mothur.align.report" from_work_dir="alignreport_in*.good.dat" label="${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 ${on_string}: count">
+        <data name="count_out" format="mothur.count_table" from_work_dir="count_in*.good.dat" label="${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="fasta_in" value="Mock_S280_L001_R1_001_small.trim.contigs.fasta" ftype="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"/>
+            <output name="fasta_out" file="Mock_S280_L001_R1_001_small.trim.contigs.good.fasta" ftype="fasta"/>
+            <output name="bad_accnos" file="Mock_S280_L001_R1_001_small.trim.contigs.bad.accnos" ftype="mothur.accnos"/>
             <expand macro="logfile-test"/>
         </test>
         <test>
-            <param name="fasta_in" value="amazon.fasta"/>
+            <param name="fasta_in" value="amazon.fasta" ftype="mothur.align"/>
             <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"/>
+            <output name="fasta_out" md5="d41d8cd98f00b204e9800998ecf8427e" ftype="mothur.align"/>
+            <output name="count_out" md5="5f4a08bbf3ec12f954edbcc6b2a2feee" ftype="mothur.count_table"/>
+            <output name="bad_accnos" md5="66acde5349e34fc97be22032ce68eea5" ftype="mothur.accnos"/>
             <expand macro="logfile-test"/>
         </test>
     </tests>
@@ -143,14 +147,14 @@
 
 @MOTHUR_OVERVIEW@
 
-**Command Documenation**
+**Command Documentation**
 
 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
+.. _name: https://www.mothur.org/wiki/Name_file
+.. _group: https://www.mothur.org/wiki/Group_file
+.. _align.report: https://www.mothur.org/wiki/Align.seqs
+.. _screen.seqs: https://www.mothur.org/wiki/Screen.seqs
 
 ]]>
     </help>