# HG changeset patch # User iracooke # Date 1362462459 18000 # Node ID f16d641313717fa804c916e76369b566acad7026 # Parent a5414905da0f4135606c705c05bc2908ba9fd9cf Uploaded diff -r a5414905da0f -r f16d64131371 README --- a/README Tue Mar 05 00:38:28 2013 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,5 +0,0 @@ -This package installs a wrapper script for the X!Tandem search engine - -Requirements: -This package depends on the galaxy_protk and protk_trans_proteomic_pipeline packages -Please see instructions for those packages before installing diff -r a5414905da0f -r f16d64131371 repository_dependencies.xml --- a/repository_dependencies.xml Tue Mar 05 00:38:28 2013 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,16 +0,0 @@ - - - - - - - - - - - - diff -r a5414905da0f -r f16d64131371 tandem.xml --- a/tandem.xml Tue Mar 05 00:38:28 2013 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,143 +0,0 @@ - - - - galaxy_protk - trans_proteomic_pipeline - - - Run an X!Tandem Search - - - #if $database.source_select=="built_in": - rvm 1.9.3@protk-1.2.0 do tandem_search.rb -d $database.dbkey - #else #rvm 1.9.3@protk-1.2.0 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 - - - - - - - - - - - - Database - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Missed Cleavages Allowed - - - - - - - Enzyme - - - - - - - - Precursor Ion Tolerance Units - - - - - - - - - - - - - - - - - - - - - - - - - - - - -**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 a5414905da0f -r f16d64131371 test-data/bsa.fasta --- a/test-data/bsa.fasta Tue Mar 05 00:38:28 2013 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,26 +0,0 @@ ->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 a5414905da0f -r f16d64131371 test-data/bsa.mzML --- a/test-data/bsa.mzML Tue Mar 05 00:38:28 2013 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,96 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 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 - - - - - - AABIQgAAUEIAAMpCAABkQwAA8EEAACBCAEAHRQAAgEIAACRDAICRQwAAhEIAAE9EAADwQQAAjkIAAAhCAAAEQgAAMEIAAChDAACmQgAA4EEAAJBDAADGQgAA1EIAAHhCAAAEQwAAHEMAAKpCAAAcQgAAgUMAALRCAIDuQwAADEIAAJxCAMCERAAAOEIAADlDAAAAQgAA3kIAAPxCAICfQwAASUMAAAtDAADoQQAA00MAgMNDAADoQQAA+UMAAOBBAABUQgAAH0MAAExCAICFQwAA+EEAABxCAACMQgAAIEIAAKhCAIDVQwAAKEMAAFpEAAAIQgAABEIAAOBBAAAMQgAA4EEAAIpCAAA1QwAA+EIAAFBCAADoQQAAEEIAACRCAIC8QwAAFUQAAKRDAAAkQgAAgUMAAAhCAIDFQwAA9kIAAOhBAADEQgAAFEMAAAxCAADUQgAAO0MAAApDAADgQQAA8EEAAANDAEAmRAAACEIAAL5CAAASRAAAAEIAABFDAEBQRA== - - - - - - - - - 2685 - - - 7058 - b76171188a63cfad075d3738a172b15f1f9e0c4c - diff -r a5414905da0f -r f16d64131371 test-data/bsa.pepXML --- a/test-data/bsa.pepXML Tue Mar 05 00:38:28 2013 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,133 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff -r a5414905da0f -r f16d64131371 tool-data/pepxml_databases.loc.sample --- a/tool-data/pepxml_databases.loc.sample Tue Mar 05 00:38:28 2013 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,13 +0,0 @@ -#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 a5414905da0f -r f16d64131371 tool-data/repository_dependencies.xml --- a/tool-data/repository_dependencies.xml Tue Mar 05 00:38:28 2013 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,8 +0,0 @@ - - - - - \ No newline at end of file diff -r a5414905da0f -r f16d64131371 tool-data/tandem.xml --- a/tool-data/tandem.xml Tue Mar 05 00:38:28 2013 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,143 +0,0 @@ - - - - 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 - - - - - - - - - - - - Database - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Missed Cleavages Allowed - - - - - - - Enzyme - - - - - - - - Precursor Ion Tolerance Units - - - - - - - - - - - - - - - - - - - - - - - - - - - - -**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 a5414905da0f -r f16d64131371 tool-data/tandem_mods.loc.sample --- a/tool-data/tandem_mods.loc.sample Tue Mar 05 00:38:28 2013 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,6 +0,0 @@ -#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 a5414905da0f -r f16d64131371 tool-data/test-data/bsa.fasta --- a/tool-data/test-data/bsa.fasta Tue Mar 05 00:38:28 2013 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,26 +0,0 @@ ->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 a5414905da0f -r f16d64131371 tool-data/test-data/bsa.mzML --- a/tool-data/test-data/bsa.mzML Tue Mar 05 00:38:28 2013 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,96 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 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 - - - - - - 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 - - - - - - - - - 2685 - - - 7058 - b76171188a63cfad075d3738a172b15f1f9e0c4c - diff -r a5414905da0f -r f16d64131371 tool-data/test-data/bsa.pepXML --- a/tool-data/test-data/bsa.pepXML Tue Mar 05 00:38:28 2013 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,133 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff -r a5414905da0f -r f16d64131371 tool-data/tool-data/pepxml_databases.loc.sample --- a/tool-data/tool-data/pepxml_databases.loc.sample Tue Mar 05 00:38:28 2013 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,13 +0,0 @@ -#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 a5414905da0f -r f16d64131371 tool-data/tool-data/tandem_mods.loc.sample --- a/tool-data/tool-data/tandem_mods.loc.sample Tue Mar 05 00:38:28 2013 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,6 +0,0 @@ -#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 a5414905da0f -r f16d64131371 tool-data/tool_dependencies.xml --- a/tool-data/tool_dependencies.xml Tue Mar 05 00:38:28 2013 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,21 +0,0 @@ - - - - - - - - - - - - - - \ No newline at end of file diff -r a5414905da0f -r f16d64131371 tool_dependencies.xml --- a/tool_dependencies.xml Tue Mar 05 00:38:28 2013 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,21 +0,0 @@ - - - - - - - - - - - - - - \ No newline at end of file