# HG changeset patch
# User iracooke
# Date 1362379882 18000
# Node ID 5d2228f63b53f0659c1be5dfc68312b9bb607d66
# Parent b4123e38df43c9734c151d98ddbd0905c179514e
Uploaded
diff -r b4123e38df43 -r 5d2228f63b53 repository_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/repository_dependencies.xml Mon Mar 04 01:51:22 2013 -0500
@@ -0,0 +1,8 @@
+
+
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+
\ No newline at end of file
diff -r b4123e38df43 -r 5d2228f63b53 tandem.xml
--- a/tandem.xml Sun Jan 06 19:12:02 2013 -0500
+++ b/tandem.xml Mon Mar 04 01:51:22 2013 -0500
@@ -1,11 +1,16 @@
- protkgem
+
+
+ galaxy_protk
+ trans_proteomic_pipeline
+
+
Run an X!Tandem Search
#if $database.source_select=="built_in":
- tandem_search.rb -d $database.dbkey
- #else #tandem_search.rb -d $database.fasta_file
+ rvm 1.9.3@protk-1.1.9 do tandem_search.rb -d $database.dbkey
+ #else #rvm 1.9.3@protk-1.1.9 do tandem_search.rb -d $database.fasta_file
#end if
--var-mods='
@@ -24,8 +29,6 @@
$input_file -o $output -r --enzyme=$enzyme --precursor-ion-tol-units=$precursor_tolu -v $missed_cleavages -f $fragment_ion_tol -p $precursor_ion_tol $allow_multi_isotope_search --keep-params-files
-
-
@@ -110,6 +113,18 @@
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diff -r b4123e38df43 -r 5d2228f63b53 test-data/bsa.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bsa.fasta Mon Mar 04 01:51:22 2013 -0500
@@ -0,0 +1,26 @@
+>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
\ No newline at end of file
diff -r b4123e38df43 -r 5d2228f63b53 test-data/bsa.mzML
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bsa.mzML Mon Mar 04 01:51:22 2013 -0500
@@ -0,0 +1,96 @@
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+ 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
+
+
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+ 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
+
+
+
+
+
+
+
+
+ 2685
+
+
+ 7058
+ b76171188a63cfad075d3738a172b15f1f9e0c4c
+
diff -r b4123e38df43 -r 5d2228f63b53 test-data/bsa.pepXML
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bsa.pepXML Mon Mar 04 01:51:22 2013 -0500
@@ -0,0 +1,133 @@
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diff -r b4123e38df43 -r 5d2228f63b53 tool-data/repository_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/repository_dependencies.xml Mon Mar 04 01:51:22 2013 -0500
@@ -0,0 +1,8 @@
+
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\ No newline at end of file
diff -r b4123e38df43 -r 5d2228f63b53 tool-data/tandem.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/tandem.xml Mon Mar 04 01:51:22 2013 -0500
@@ -0,0 +1,143 @@
+
+
+
+ galaxy_protk
+ trans_proteomic_pipeline
+
+
+ Run an X!Tandem Search
+
+
+ #if $database.source_select=="built_in":
+ rvm 1.9.3@protk-1.1.9 do tandem_search.rb -d $database.dbkey
+ #else #rvm 1.9.3@protk-1.1.9 do tandem_search.rb -d $database.fasta_file
+ #end if
+
+ --var-mods='
+ $variable_mods
+ #for $custom_variable_mod in $custom_variable_mods:
+ ,${custom_variable_mod.custom_mod}
+ #end for
+ '
+
+ --fix-mods='
+ $fixed_mods
+ #for $custom_fix_mod in $custom_fix_mods:
+ ,${custom_fix_mod.custom_mod}
+ #end for
+ '
+
+ $input_file -o $output -r --enzyme=$enzyme --precursor-ion-tol-units=$precursor_tolu -v $missed_cleavages -f $fragment_ion_tol -p $precursor_ion_tol $allow_multi_isotope_search --keep-params-files
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+**What it does**
+
+Runs an MS/MS database search using the X!Tandem search engine. Output is in the form of a pepXML file containing identified peptides along with their raw search scores.
+
+----
+
+**References**
+
+Please see http://www.thegpm.org/GPM/references.html for details of references describing the X!Tandem search engine.
+
+
+
+
diff -r b4123e38df43 -r 5d2228f63b53 tool-data/test-data/bsa.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/test-data/bsa.fasta Mon Mar 04 01:51:22 2013 -0500
@@ -0,0 +1,26 @@
+>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
\ No newline at end of file
diff -r b4123e38df43 -r 5d2228f63b53 tool-data/test-data/bsa.mzML
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/test-data/bsa.mzML Mon Mar 04 01:51:22 2013 -0500
@@ -0,0 +1,96 @@
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+ 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
+
+
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+ 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
+
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+
+
+
+ 2685
+
+
+ 7058
+ b76171188a63cfad075d3738a172b15f1f9e0c4c
+
diff -r b4123e38df43 -r 5d2228f63b53 tool-data/test-data/bsa.pepXML
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/test-data/bsa.pepXML Mon Mar 04 01:51:22 2013 -0500
@@ -0,0 +1,133 @@
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diff -r b4123e38df43 -r 5d2228f63b53 tool-data/tool-data/pepxml_databases.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/tool-data/pepxml_databases.loc.sample Mon Mar 04 01:51:22 2013 -0500
@@ -0,0 +1,13 @@
+#This file lists the names of protein databases installed locally in protk.
+# These are used by omssa and x!tandem as well as the "mascot to pepxml" tool
+# In order to combine search results with Interprophet searches must be run against an identical database
+#
+# Entries should follow the be structured as follows
+# Display_name omssa_tandem_dbname dbkey
+#
+#
+Swissprot spall_ spall spall_
+Combined PlasmboDB (falciparum) and Swissprot Human plasmodb_pfalciparum_sphuman_ plasmodb_pfalciparum_sphuman plasmodb_pfalciparum_sphuman_
+Swissprot Human sphuman_ sphuman sphuman_
+Combined Swissprot/TRembl Human sptrhuman_ sptrhuman sptrhuman_
+Swissprot Mouse spmouse_ spmouse spmouse_
diff -r b4123e38df43 -r 5d2228f63b53 tool-data/tool-data/tandem_mods.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/tool-data/tandem_mods.loc.sample Mon Mar 04 01:51:22 2013 -0500
@@ -0,0 +1,6 @@
+#This file lists the names of inbuilt chemical modifications accepted by X!Tandem
+#
+#
+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
diff -r b4123e38df43 -r 5d2228f63b53 tool-data/tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/tool_dependencies.xml Mon Mar 04 01:51:22 2013 -0500
@@ -0,0 +1,21 @@
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\ No newline at end of file
diff -r b4123e38df43 -r 5d2228f63b53 tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml Mon Mar 04 01:51:22 2013 -0500
@@ -0,0 +1,21 @@
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\ No newline at end of file