--- a/tools/seq_primer_clip/seq_primer_clip.xml	Thu Nov 21 10:47:23 2013 -0500
+++ b/tools/seq_primer_clip/seq_primer_clip.xml	Thu Feb 02 11:52:37 2017 -0500
@@ -1,20 +1,21 @@
-<tool id="seq_primer_clip" name="Primer clip sequences" version="0.0.10">
+<tool id="seq_primer_clip" name="Primer clip sequences" version="0.0.14">
     <description>Trim off 5' or 3' primers</description>
     <requirements>
-        <requirement type="package" version="1.62">biopython</requirement>
+        <requirement type="package" version="1.0.1">galaxy_sequence_utils</requirement>
+        <requirement type="package" version="1.67">biopython</requirement>
         <requirement type="python-module">Bio</requirement>
     </requirements>
-    <version_command interpreter="python">seq_primer_clip.py --version</version_command>   
-    <command interpreter="python">
-seq_primer_clip.py $input_file $input_file.ext $primer_fasta $primer_type $mm $min_len $keep_negatives $output_file
-    </command>
     <stdio>
         <!-- Anything other than zero is an error -->
         <exit_code range="1:" />
         <exit_code range=":-1" />
     </stdio>
+    <version_command interpreter="python">seq_primer_clip.py --version</version_command>   
+    <command interpreter="python">
+seq_primer_clip.py $input_file $input_file.ext $primer_fasta $primer_type $mm $min_len $keep_negatives $output_file
+    </command>
     <inputs>
-        <param name="input_file" type="data" format="fasta,fastq,sff" label="Sequence file to clip" description="FASTA, FASTQ, or SFF format."/>
+        <param name="input_file" type="data" format="fasta,fastq,sff" label="Sequence file to clip" help="FASTA, FASTQ, or SFF format."/>
         <param name="primer_fasta" type="data" format="fasta" label="FASTA file containing primer(s)"/>
         <param name="primer_type" type="select" label="Type of primers">
             <option value="Forward">Forward (5') primers</option>
@@ -28,18 +29,7 @@
         <param name="min_len" type="integer" label="Minimum length for (clipped) sequences " value="1"/>
     </inputs>
     <outputs>
-        <data name="output_file" format="data" label="$primer_type primer clipped">
-            <!-- TODO - Replace this with format="input:input_fastq" if/when that works -->
-            <change_format>
-                <when input_dataset="input_file" attribute="extension" value="sff" format="sff" />
-                <when input_dataset="input_file" attribute="extension" value="fasta" format="fasta" />
-                <when input_dataset="input_file" attribute="extension" value="fastq" format="fastq" />
-                <when input_dataset="input_file" attribute="extension" value="fastqsanger" format="fastqsanger" />
-                <when input_dataset="input_file" attribute="extension" value="fastqsolexa" format="fastqsolexa" />
-                <when input_dataset="input_file" attribute="extension" value="fastqillumina" format="fastqillumina" />
-                <when input_dataset="input_file" attribute="extension" value="fastqcssanger" format="fastqcssanger" />
-            </change_format>
-        </data>
+        <data name="output_file" format_source="input_file" metadata_source="input_file" label="$primer_type primer clipped"/>
     </outputs>
     <tests>
         <test>
@@ -97,9 +87,6 @@
             <output name="output_file" file="MID4_GLZRM4E04_rnd30_frclip.sff" ftype="sff" />
         </test>
     </tests>
-    <requirements>
-        <requirement type="python-module">Bio</requirement>
-    </requirements>
     <help>
 
 **What it does**
@@ -140,4 +127,7 @@
 This tool is available to install into other Galaxy Instances via the Galaxy
 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/seq_primer_clip 
     </help>
+    <citations>
+        <citation type="doi">10.1093/bioinformatics/btp163</citation>
+    </citations>
 </tool>