# HG changeset patch
# User iracooke
# Date 1445383700 14400
# Node ID 84b15e316fcc65be8226035ccf47007dc553634d
# Parent fa4ed0c996d95ad45fd5c391c159f834341f8797
planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/make_protein_decoys/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
diff -r fa4ed0c996d9 -r 84b15e316fcc README.md
--- 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
-
-
diff -r fa4ed0c996d9 -r 84b15e316fcc README.rst
--- /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_
+
diff -r fa4ed0c996d9 -r 84b15e316fcc make_decoy.xml
--- 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 @@
-
-
- protk
-
-
-
- Generate random protein sequences with the same AA composition as input sequences
-
-
-
- make_decoy.rb $fasta_file -o $output -P $prefix_string $append
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+
+ Generate random protein sequences with the same AA composition as input sequences
+
+
+ iracooke/protk-1.4.3
+ protk
+
+
+
+
+
+ make_decoy.rb $fasta_file -o $output -P $prefix_string $append
+
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+
**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
-
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+
diff -r fa4ed0c996d9 -r 84b15e316fcc repository_dependencies.xml
--- 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 @@
-
-
-
-
diff -r fa4ed0c996d9 -r 84b15e316fcc test-data/testdb.fasta
--- /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
diff -r fa4ed0c996d9 -r 84b15e316fcc tool_dependencies.xml
--- /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 @@
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