# HG changeset patch
# User iracooke
# Date 1427414033 14400
# Node ID 9d6e0ad4d60071981642906c4769a68b6f0dcaed
# Parent c60d1f18fd85f979dcaacf59a243cdf1d51cbb33
Docker support and update for protk 1.4
diff -r c60d1f18fd85 -r 9d6e0ad4d600 README
--- a/README Tue Jul 01 11:06:33 2014 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-Galaxy wrapper for running the X!Tandem search engine and converting results to pepXML
-
-Requirements:
-This package uses protk and the trans_proteomic_pipeline. These must be installed separately.
-
-For instructions please see: https://github.com/iracooke/protk/#galaxy-integration
\ No newline at end of file
diff -r c60d1f18fd85 -r 9d6e0ad4d600 README.rst
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/README.rst Thu Mar 26 19:53:53 2015 -0400
@@ -0,0 +1,39 @@
+X!Tandem
+========
+
+Galaxy wrapper for running the X!Tandem search engine and converting results to pepXML
+
+Requirements
+------------
+
+This package uses protk_ and the trans_proteomic_pipeline_ which need to be present in order for the tool to work.
+
+.. _protk: https://github.com/iracooke/protk
+.. _trans_proteomic_pipeline: http://tools.proteomecenter.org/wiki/index.php?title=Software:TPP
+
+There are two ways you can satify these dependencies (choose one):
+
+1. **Manual Install:** Details on how to install protk_ and the trans_proteomic_pipeline_ manually are available here_.
+
+2. **Use Docker:** These tools are 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_
+
+
+Please visit the XTandem_ page on the GPM website for details of the search engine itself.
+
+.. _XTandem: http://www.thegpm.org/tandem/
+
diff -r c60d1f18fd85 -r 9d6e0ad4d600 repository_dependencies.xml
--- a/repository_dependencies.xml Tue Jul 01 11:06:33 2014 -0400
+++ b/repository_dependencies.xml Thu Mar 26 19:53:53 2015 -0400
@@ -1,4 +1,4 @@
-
+
diff -r c60d1f18fd85 -r 9d6e0ad4d600 tandem.xml
--- a/tandem.xml Tue Jul 01 11:06:33 2014 -0400
+++ b/tandem.xml Thu Mar 26 19:53:53 2015 -0400
@@ -1,7 +1,8 @@
-
+
- protk
+ iracooke/protk-1.4.1
+ protk
Run an X!Tandem Search
@@ -44,7 +45,7 @@
-f $fragment_ion_tol
- -p $precursor_ion_tol
+ -p $precursor_ion_tol
$allow_multi_isotope_search
@@ -86,9 +87,9 @@
-
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@@ -132,7 +133,7 @@
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@@ -143,42 +144,42 @@
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@@ -187,7 +188,19 @@
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+
**What it does**
diff -r c60d1f18fd85 -r 9d6e0ad4d600 tandem_to_pepxml.xml
--- a/tandem_to_pepxml.xml Tue Jul 01 11:06:33 2014 -0400
+++ b/tandem_to_pepxml.xml Thu Mar 26 19:53:53 2015 -0400
@@ -1,25 +1,38 @@
-
+
- protk
- trans_proteomic_pipeline
-
+ iracooke/protk-1.4.1
+ protk
+ trans_proteomic_pipeline
+
- Converts a tandem result file to pepXML
+ Converts a tandem result file to pepXML
-
- tandem_to_pepxml.rb $input_file -o $output
-
+
+ tandem_to_pepxml.rb $input_file -o $output
+
+
+
+
+
-
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+ Convert X!Tandem results to pepXML
+
-
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- Convert X!Tandem results to pepXML
-
+
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+
diff -r c60d1f18fd85 -r 9d6e0ad4d600 test-data/tandem_to_pepxml_test.tandem
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tandem_to_pepxml_test.tandem Thu Mar 26 19:53:53 2015 -0400
@@ -0,0 +1,1145 @@
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+ yes
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+ yes
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+ no
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+ no
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+ 2
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+ no
+ yes
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+ 600.0
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+ /Users/icooke/Desktop/iptest/mr176-BSA100fmole_BA3_01_8167.d.mgf
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+ yes
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+ no
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+ 10
+ no
+ no
+ no
+ 4000.0
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+ /Users/icooke/Desktop/iptest/AASequences.fasta
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+ 528901
+ 33
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diff -r c60d1f18fd85 -r 9d6e0ad4d600 test-data/testdb.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/testdb.fasta Thu Mar 26 19:53:53 2015 -0400
@@ -0,0 +1,38 @@
+>sp|ALBU_BOVIN|
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+VASLRETYGDMADCCEKQEPERNECFLSHKDDSPDLPKLKPDPNTLCDEF
+KADEKKFWGKYLYEIARRHPYFYAPELLYYANKYNGVFQECCQAEDKGAC
+LLPKIETMREKVLASSARQRLRCASIQKFGERALKAWSVARLSQKFPKAE
+FVEVTKLVTDLTKVHKECCHGDLLECADDRADLAKYICDNQDTISSKLKE
+CCDKPLLEKSHCIAEVEKDAIPENLPPLTADFAEDKDVCKNYQEAKDAFL
+GSFLYEYSRRHPEYAVSVLLRLAKEYEATLEECCAKDDPHACYSTVFDKL
+KHLVDEPQNLIKQNCDQFEKLGEYGFQNALIVRYTRKVPQVSTPTLVEVS
+RSLGKVGTRCCTKPESERMPCTEDYLSLILNRLCVLHEKTPVSEKVTKCC
+TESLVNRRPCFSALTPDETYVPKAFDEKLFTFHADICTLPDTEKQIKKQT
+ALVELLKHKPKATEEQLKTVMENFVAFVDKCCAADDKEACFAVEGPKLVV
+STQTALA
+>sp|AMYS_HUMAN|
+MKLFWLLFTIGFCWAQYSSNTQQGRTSIVHLFEWRWVDIALECERYLAPK
+GFGGVQVSPPNENVAIHNPFRPWWERYQPVSYKLCTRSGNEDEFRNMVTR
+CNNVGVRIYVDAVINHMCGNAVSAGTSSTCGSYFNPGSRDFPAVPYSGWD
+FNDGKCKTGSGDIENYNDATQVRDCRLSGLLDLALGKDYVRSKIAEYMNH
+LIDIGVAGFRIDASKHMWPGDIKAILDKLHNLNSNWFPEGSKPFIYQEVI
+DLGGEPIKSSDYFGNGRVTEFKYGAKLGTVIRKWNGEKMSYLKNWGEGWG
+FMPSDRALVFVDNHDNQRGHGAGGASILTFWDARLYKMAVGFMLAHPYGF
+TRVMSSYRWPRYFENGKDVNDWVGPPNDNGVTKEVTINPDTTCGNDWVCE
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+FSLTLQTGLPAGTYCDVISGDKINGNCTGIKIYVSDDGKAHFSISNSAED
+PFIAIHAESKL
+>sp|CAS1_BOVIN|
+MKLLILTCLVAVALARPKHPIKHQGLPQEVLNENLLRFFVAPFPEVFGKE
+KVNELSKDIGSESTEDQAMEDIKQMEAESISSSEEIVPNSVEQKHIQKED
+VPSERYLGYLEQLLRLKKYKVPQLEIVPNSAEERLHSMKEGIHAQQKEPM
+IGVNQELAYFYPELFRQFYQLDAYPSGAWYYVPLGTQYTDAPSFSDIPNP
+IGSENSEKTTMPLW
+>sp|CAS2_BOVIN|
+MKFFIFTCLLAVALAKNTMEHVSSSEESIISQETYKQEKNMAINPSKENL
+CSTFCKEVVRNANEEEYSIGSSSEESAEVATEEVKITVDDKHYQKALNEI
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+KKTVDMESTEVFTKKTKLTEEEKNRLNFLKKISQRYQKFALPQYLKTVYQ
+HQKAMKPWIQPKTKVIPYVRYL
\ No newline at end of file
diff -r c60d1f18fd85 -r 9d6e0ad4d600 test-data/tiny.mzML
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tiny.mzML Thu Mar 26 19:53:53 2015 -0400
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diff -r c60d1f18fd85 -r 9d6e0ad4d600 tool-data/tandem_mods.loc.sample
--- a/tool-data/tandem_mods.loc.sample Tue Jul 01 11:06:33 2014 -0400
+++ b/tool-data/tandem_mods.loc.sample Thu Mar 26 19:53:53 2015 -0400
@@ -3,4 +3,5 @@
#
Carbamidomethyl C carbamidomethyl_c_ 57.021464@C carbamidomethyl_c_
Glycocapture-N glycocapture_n_ 0.998@N!{P}[ST] glycocapture_n_
-Oxidation M oxidation_m_ 15.994915@M oxidation_m_
\ No newline at end of file
+Oxidation M oxidation_m_ 15.994915@M oxidation_m_
+Biotin K biotin_k_ 226.077598@K biotin_k_
\ No newline at end of file