Mercurial > repos > iracooke > make_protein_decoys

changeset 1:354e820eb485 draft

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Docker support and update for protk 1.4
author iracooke
date Thu, 26 Mar 2015 21:27:53 -0400
parents a90539d8e409
children bd4844c664f2
files README README.md README.rst make_decoy.xml repository_dependencies.xml test-data/testdb.fasta
diffstat 6 files changed, 86 insertions(+), 9 deletions(-) [+]
line wrap: on
line diff
--- 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
--- 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
-
-
--- /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_
+
--- 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>
 
--- 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>
--- /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