--- a/README.md	Fri Jun 13 18:03:01 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,3 +0,0 @@
-# Make decoys from a protein database
-
-

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.rst	Tue Oct 20 19:28:20 2015 -0400
@@ -0,0 +1,33 @@
+Make Decoys
+===========
+
+Create decoy sequences for tandem ms searching
+
+Requirements
+------------
+
+This package uses protk_ which needs to be present in order for the tool to work.
+
+.. _protk: https://github.com/iracooke/protk
+
+There are two ways you can satify this dependency (choose one):
+
+1. **Manual Install:** Details on how to install protk_ manually are available here_.
+
+2. **Use Docker:** This tool is designed to run inside a docker_ container. If your galaxy supports `running tools within a docker container`__ you don't need to worry about dependencies. Simply install and things should just work.  The docker container itself is versioned and new versions of this tool will automatically download an update to the container if needed.
+
+.. _docker: https://www.docker.com/
+.. _here: https://github.com/iracooke/protk/#galaxy-integration
+.. _container: https://wiki.galaxyproject.org/Admin/Tools/Docker
+__ container_
+
+
+Further Info
+------------
+
+The source code for this tool and other protk galaxy tools is on github_.  Please visit the github page to contribute to the project or to `report an issue`__ 
+
+.. _github: https://github.com/iracooke/protk-galaxytools
+.. _issue: https://github.com/iracooke/protk-galaxytools/issues
+__ issue_
+

--- a/make_decoy.xml	Fri Jun 13 18:03:01 2014 -0400
+++ b/make_decoy.xml	Tue Oct 20 19:28:20 2015 -0400
@@ -1,38 +1,41 @@
-<tool id="make_decoy" name="Generate protein decoy sequences" version="1.0.0">
-	<requirements>
-	    <requirement type="package" version="1.3">protk</requirement>
-   </requirements>
-
-	<description>
-		Generate random protein sequences with the same AA composition as input sequences
-	</description>
-
-	<command>
-		make_decoy.rb $fasta_file -o $output -P $prefix_string $append
-	</command>
-
-	<stdio>
-		<exit_code range="1:"   level="fatal"   description="Failure" />
-	</stdio>
-
-	<inputs>	
-		<param name="fasta_file" type="data" format="fasta" label="Fasta file contain protein sequences" />
-		<param name="prefix_string" help="Prefix String to use for Decoys" type="text" value="decoy_" label="Prefix String" size="20"/>		
-		<param name="append" type="boolean" label="Append input sequences to the generated sequences" help="" truevalue="--append" falsevalue="" />
-	</inputs>
-
-	<outputs>
-		<data format="fasta" name="output" />
-	</outputs>
-
-
-  <help>
+<tool id="make_decoy" name="Generate protein decoy sequences" version="1.0.1">
+    <description>
+        Generate random protein sequences with the same AA composition as input sequences
+    </description>
+    <requirements>
+        <container type="docker">iracooke/protk-1.4.3</container>
+        <requirement type="package" version="1.4.3">protk</requirement>
+    </requirements>
+    <stdio>
+        <exit_code range="1:" level="fatal" description="Failure" />
+    </stdio>
+    <command>
+        make_decoy.rb $fasta_file -o $output -P $prefix_string $append
+    </command>
+    <inputs>
+        <param name="fasta_file" type="data" format="fasta" label="Fasta file contain protein sequences" />
+        <param name="prefix_string" help="Prefix String to use for Decoys" type="text" value="decoy_" label="Prefix String" size="20"/>        
+        <param name="append" type="boolean" label="Append input sequences to the generated sequences" help="" truevalue="--append" falsevalue="" />
+    </inputs>
+    <outputs>
+        <data format="fasta" name="output" />
+    </outputs>
+    <tests>
+      <test>
+          <param name="fasta_file" value="testdb.fasta" format="fasta"/>
+          <output name="output" format="fasta">
+              <assert_contents>
+                  <has_text text="decoy_rp3" />
+              </assert_contents>
+          </output>
+      </test>
+    </tests>
+    <help>
 
 **What it does**
 
 Generates random protein sequences based on the amino acid composition of a given set of input sequences. To be used for decoy proteomics searches
 
 
-  </help>
-
+    </help>
 </tool>

--- a/repository_dependencies.xml	Fri Jun 13 18:03:01 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,4 +0,0 @@
-<?xml version="1.0"?>
-<repositories description="Proteomics datatypes">
-    <repository changeset_revision="a1b29f86bdbf" name="proteomics_datatypes" owner="iracooke" toolshed="https://testtoolshed.g2.bx.psu.edu" />
- </repositories>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/testdb.fasta	Tue Oct 20 19:28:20 2015 -0400
@@ -0,0 +1,38 @@
+>sp|ALBU_BOVIN|
+MKWVTFISLLLLFSSAYSRGVFRRDTHKSEIAHRFKDLGEEHFKGLVLIA
+FSQYLQQCPFDEHVKLVNELTEFAKTCVADESHAGCEKSLHTLFGDELCK
+VASLRETYGDMADCCEKQEPERNECFLSHKDDSPDLPKLKPDPNTLCDEF
+KADEKKFWGKYLYEIARRHPYFYAPELLYYANKYNGVFQECCQAEDKGAC
+LLPKIETMREKVLASSARQRLRCASIQKFGERALKAWSVARLSQKFPKAE
+FVEVTKLVTDLTKVHKECCHGDLLECADDRADLAKYICDNQDTISSKLKE
+CCDKPLLEKSHCIAEVEKDAIPENLPPLTADFAEDKDVCKNYQEAKDAFL
+GSFLYEYSRRHPEYAVSVLLRLAKEYEATLEECCAKDDPHACYSTVFDKL
+KHLVDEPQNLIKQNCDQFEKLGEYGFQNALIVRYTRKVPQVSTPTLVEVS
+RSLGKVGTRCCTKPESERMPCTEDYLSLILNRLCVLHEKTPVSEKVTKCC
+TESLVNRRPCFSALTPDETYVPKAFDEKLFTFHADICTLPDTEKQIKKQT
+ALVELLKHKPKATEEQLKTVMENFVAFVDKCCAADDKEACFAVEGPKLVV
+STQTALA
+>sp|AMYS_HUMAN|
+MKLFWLLFTIGFCWAQYSSNTQQGRTSIVHLFEWRWVDIALECERYLAPK
+GFGGVQVSPPNENVAIHNPFRPWWERYQPVSYKLCTRSGNEDEFRNMVTR
+CNNVGVRIYVDAVINHMCGNAVSAGTSSTCGSYFNPGSRDFPAVPYSGWD
+FNDGKCKTGSGDIENYNDATQVRDCRLSGLLDLALGKDYVRSKIAEYMNH
+LIDIGVAGFRIDASKHMWPGDIKAILDKLHNLNSNWFPEGSKPFIYQEVI
+DLGGEPIKSSDYFGNGRVTEFKYGAKLGTVIRKWNGEKMSYLKNWGEGWG
+FMPSDRALVFVDNHDNQRGHGAGGASILTFWDARLYKMAVGFMLAHPYGF
+TRVMSSYRWPRYFENGKDVNDWVGPPNDNGVTKEVTINPDTTCGNDWVCE
+HRWRQIRNMVNFRNVVDGQPFTNWYDNGSNQVAFGRGNRGFIVFNNDDWT
+FSLTLQTGLPAGTYCDVISGDKINGNCTGIKIYVSDDGKAHFSISNSAED
+PFIAIHAESKL
+>sp|CAS1_BOVIN|
+MKLLILTCLVAVALARPKHPIKHQGLPQEVLNENLLRFFVAPFPEVFGKE
+KVNELSKDIGSESTEDQAMEDIKQMEAESISSSEEIVPNSVEQKHIQKED
+VPSERYLGYLEQLLRLKKYKVPQLEIVPNSAEERLHSMKEGIHAQQKEPM
+IGVNQELAYFYPELFRQFYQLDAYPSGAWYYVPLGTQYTDAPSFSDIPNP
+IGSENSEKTTMPLW
+>sp|CAS2_BOVIN|
+MKFFIFTCLLAVALAKNTMEHVSSSEESIISQETYKQEKNMAINPSKENL
+CSTFCKEVVRNANEEEYSIGSSSEESAEVATEEVKITVDDKHYQKALNEI
+NQFYQKFPQYLQYLYQGPIVLNPWDQVKRNAVPITPTLNREQLSTSEENS
+KKTVDMESTEVFTKKTKLTEEEKNRLNFLKKISQRYQKFALPQYLKTVYQ
+HQKAMKPWIQPKTKVIPYVRYL
\ No newline at end of file

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Tue Oct 20 19:28:20 2015 -0400
@@ -0,0 +1,6 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="protk" version="1.4.3">
+        <repository changeset_revision="b8f1acb3b933" name="package_protk_1_4_3" owner="iracooke" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
+</tool_dependency>