# HG changeset patch
# User iracooke
# Date 1427419673 14400
# Node ID 354e820eb485b0adcb689ef499334d7a6e9d551a
# Parent  a90539d8e40969a36941f25f135a18a3a47436f3
Docker support and update for protk 1.4

diff -r a90539d8e409 -r 354e820eb485 README
--- a/README	Fri Jun 13 18:10:03 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,4 +0,0 @@
-Requirements:
-This package uses protk which must be installed separately. 
-
-For instructions please see: https://github.com/iracooke/protk/#galaxy-integration
\ No newline at end of file
diff -r a90539d8e409 -r 354e820eb485 README.md
--- a/README.md	Fri Jun 13 18:10:03 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,3 +0,0 @@
-# Make decoys from a protein database
-
-
diff -r a90539d8e409 -r 354e820eb485 README.rst
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.rst	Thu Mar 26 21:27:53 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_
+
diff -r a90539d8e409 -r 354e820eb485 make_decoy.xml
--- a/make_decoy.xml	Fri Jun 13 18:10:03 2014 -0400
+++ b/make_decoy.xml	Thu Mar 26 21:27:53 2015 -0400
@@ -1,6 +1,7 @@
 <tool id="make_decoy" name="Generate protein decoy sequences" version="1.0.0">
 	<requirements>
-	    <requirement type="package" version="1.3">protk</requirement>
+		<container type="docker">iracooke/protk-1.4.1</container>
+	    <requirement type="package" version="1.4">protk</requirement>
    </requirements>
 
 	<description>
@@ -25,6 +26,18 @@
 		<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>
 
diff -r a90539d8e409 -r 354e820eb485 repository_dependencies.xml
--- a/repository_dependencies.xml	Fri Jun 13 18:10:03 2014 -0400
+++ b/repository_dependencies.xml	Thu Mar 26 21:27:53 2015 -0400
@@ -1,4 +1,4 @@
 <?xml version="1.0"?>
 <repositories description="Proteomics datatypes">
-    <repository changeset_revision="f66f8ca7b7b9" name="proteomics_datatypes" owner="iracooke" toolshed="http://toolshed.g2.bx.psu.edu" />
+    <repository changeset_revision="ac51d9dbfb4d" name="proteomics_datatypes" owner="iracooke" toolshed="https://toolshed.g2.bx.psu.edu" />
  </repositories>
diff -r a90539d8e409 -r 354e820eb485 test-data/testdb.fasta
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/testdb.fasta	Thu Mar 26 21:27:53 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