| Previous changeset 9:50eb60757ca5 (2013-06-09) Next changeset 11:618d74240c7f (2014-06-16) |
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Commit message:
Uploaded |
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added:
README.md tandem_to_pepxml.xml |
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removed:
README repository_dependencies.xml tandem.xml test-data/bsa.fasta test-data/bsa.mzML test-data/bsa.pepXML tool-data/pepxml_databases.loc.sample tool-data/tandem_mods.loc.sample tool_dependencies.xml |
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| diff -r 50eb60757ca5 -r ffd1d25b8080 README --- a/README Sun Jun 09 08:19:31 2013 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -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 |
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| diff -r 50eb60757ca5 -r ffd1d25b8080 README.md --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.md Mon Jun 16 05:47:38 2014 -0400 |
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| @@ -0,0 +1,6 @@ +## What is it? +Galaxy tool definition file and wrapper scripts for the [X!Tandem search engine](http://www.thegpm.org/tandem/index.html). + +## This tool requires that the protk rubygem and X!Tandem itself are installed. + + |
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| diff -r 50eb60757ca5 -r ffd1d25b8080 repository_dependencies.xml --- a/repository_dependencies.xml Sun Jun 09 08:19:31 2013 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,5 +0,0 @@ -<?xml version="1.0"?> -<repositories description="Proteomics datatypes and the TPP"> - <repository toolshed="http://toolshed.g2.bx.psu.edu" name="proteomics_datatypes" owner="iracooke" changeset_revision="09b89b345de2"/> - <repository toolshed="http://toolshed.g2.bx.psu.edu" name="protk_trans_proteomic_pipeline" owner="iracooke" changeset_revision="e85a18371516"/> - </repositories> |
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| diff -r 50eb60757ca5 -r ffd1d25b8080 tandem.xml --- a/tandem.xml Sun Jun 09 08:19:31 2013 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,143 +0,0 @@ -<tool id="proteomics_search_tandem_1" name="X!Tandem MSMS Search" version="1.0.1"> - - <requirements> - <requirement type="package" version="1.2.2">galaxy_protk</requirement> - <requirement type="package" version="4.6.1">trans_proteomic_pipeline</requirement> - </requirements> - - <description>Run an X!Tandem Search</description> - - <command> - #if $database.source_select=="built_in": - rvm 1.9.3@protk-1.2.2 do tandem_search.rb -d $database.dbkey - #else #rvm 1.9.3@protk-1.2.2 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 - - </command> - - <inputs> - <conditional name="database"> - <param name="source_select" type="select" label="Database source"> - <option value="built_in">Built-In</option> - <option value="input_ref">Your Upload File</option> - </param> - <when value="built_in"> - <param name="dbkey" type="select" format="text" > - <label>Database</label> - <options from_file="pepxml_databases.loc"> - <column name="name" index="0" /> - <column name="value" index="2" /> - </options> - </param> - </when> - <when value="input_ref"> - <param name="fasta_file" type="data" format="fasta" label="Uploaded FASTA file" /> - </when> - </conditional> - - <param name="input_file" type="data" format="mzml" multiple="false" label="MSMS File" help="An mzML file with MS/MS data"/> - - - <param name="variable_mods" format="text" type="select" multiple="true" label="Variable Modifications" help="Hold the appropriate key while - clicking to select multiple items"> - <options from_file="tandem_mods.loc"> - <column name="name" index="0" /> - <column name="value" index="2" /> - </options> - </param> - - <repeat name="custom_variable_mods" title="Custom Variable Modifications" help="You can specify a modification when present in a motif. For instance, 0.998@N!{P}[ST] is a deamidation modification on N only if it is present in an N[any but P][S or T] motif (N-glycosite)."> - <param name="custom_mod" type="text"> - </param> - </repeat> - - - <param name="fixed_mods" format="text" type="select" multiple="true" label="Fixed Modifications" help="Hold the appropriate key while - clicking to select multiple items"> - <options from_file="tandem_mods.loc"> - <column name="name" index="0" /> - <column name="value" index="2" /> - </options> - </param> - - <repeat name="custom_fix_mods" title="Custom Fixed Modifications" help="You can specify a modification when present in a motif. For instance, 0.998@N!{P}[ST] is a deamidation modification on N only if it is present in an N[any but P][S or T] motif (N-glycosite)."> - <param name="custom_mod" type="text"> - </param> - </repeat> - - - - <param name="missed_cleavages" type="select" format="text" help="Allow peptides to contain up to this many missed enzyme cleavage sites"> - <label>Missed Cleavages Allowed</label> - <option value="0">0</option> - <option value="1">1</option> - <option value="2">2</option> - </param> - - <param name="enzyme" type="select" format="text"> - <label>Enzyme</label> - <option value="Trypsin">Trypsin</option> - </param> - - <param name="fragment_ion_tol" help="Fragment Ion Tolerance in Daltons" type="float" value="0.65" min="0" max="10000" label="Fragment ion tolerance"/> - - <param name="precursor_ion_tol" help="Precursor Ion Tolerance (Da or ppm)" type="float" value="100" min="0" max="10000" label="Precursor ion tolerance"/> - <param name="precursor_tolu" type="select" format="text"> - <label>Precursor Ion Tolerance Units</label> - <option value="ppm">ppm</option> - <option value="Da">Da</option> - </param> - - <param name="allow_multi_isotope_search" type="boolean" label="Allow multi-isotope search" help="This allows peptide candidates in windows around -1 Da and -2 Da from the acquired mass to be considered. Only applicable when the minus/plus window above is set to less than 0.5 Da. Good for accurate-mass instruments for which the reported precursor mass is not corrected to the monoisotopic mass." truevalue="" falsevalue="--strict-monoisotopic-mass"/> - - </inputs> - - - <outputs> - <data format="raw_pepxml" name="output" metadata_source="input_file" label="X!Tandem_vs_${database.dbkey if $database.has_key('dbkey') else $database.fasta_file.display_name}.${input_file.display_name}.${input_file.display_name}.pepXML"/> - </outputs> - - <tests> - <test> - <param name="source_select" value="input_ref"/> - <param name="fasta_file" value="bsa.fasta"/> - <param name="input_file" value="bsa.mzML"/> - <param name="variable_mods" value="15.994915@M"/> - <param name="fixed_mods" value="57.021464@C"/> - <param name="allow_multi_isotope_search" value="false"/> - <output name="output" file="bsa.pepXML" compare="sim_size" delta="600" /> - </test> - </tests> - - - <help> - -**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. - - </help> - -</tool> |
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| diff -r 50eb60757ca5 -r ffd1d25b8080 tandem_to_pepxml.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tandem_to_pepxml.xml Mon Jun 16 05:47:38 2014 -0400 |
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| @@ -0,0 +1,25 @@ +<tool id="tandem_to_pepxml_1" name="Tandem to pepXML" version="1.0.1"> + <requirements> + <requirement type="package" version="1.3.0">protk</requirement> + <requirement type="package" version="4.6.3">trans_proteomic_pipeline</requirement> + </requirements> + + <description>Converts a tandem result file to pepXML</description> + +<command> + tandem_to_pepxml.rb $input_file -o $output +</command> + +<inputs> + <param name="input_file" type="data" format="tandem" multiple="false" label="Input File" help="X!Tandem results file"/> +</inputs> + +<outputs> + <data format="raw_pepxml" metadata_source="input_file" name="output" label="${input_file.display_name}.pepXML" /> +</outputs> + +<help> + Convert X!Tandem results to pepXML +</help> + +</tool> |
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| diff -r 50eb60757ca5 -r ffd1d25b8080 test-data/bsa.fasta --- a/test-data/bsa.fasta Sun Jun 09 08:19:31 2013 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -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 |
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| diff -r 50eb60757ca5 -r ffd1d25b8080 test-data/bsa.mzML --- a/test-data/bsa.mzML Sun Jun 09 08:19:31 2013 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,96 +0,0 @@ -<?xml version="1.0" encoding="ISO-8859-1"?> -<indexedmzML xmlns="http://psi.hupo.org/ms/mzml" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.1_idx.xsd"> - <mzML xmlns="http://psi.hupo.org/ms/mzml" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.0.xsd" id="bsa" version="1.1.0"> - <cvList count="2"> - <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="3.30.0" URI="http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo"/> - <cv id="UO" fullName="Unit Ontology" version="12:10:2011" URI="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/unit.obo"/> - </cvList> - <fileDescription> - <fileContent> - <cvParam cvRef="MS" accession="MS:1000580" name="MSn spectrum" value=""/> - <cvParam cvRef="MS" accession="MS:1000127" name="centroid spectrum" value=""/> - </fileContent> - <sourceFileList count="1"> - <sourceFile id="bsa.mgf" name="bsa.mgf" location="file:///"> - <cvParam cvRef="MS" accession="MS:1000774" name="multiple peak list nativeID format" value=""/> - <cvParam cvRef="MS" accession="MS:1001062" name="Mascot MGF file" value=""/> - <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="92c6fa5d4ff59e2124950546a651bb9a85bbfd92"/> - </sourceFile> - </sourceFileList> - </fileDescription> - <softwareList count="1"> - <software id="pwiz_3.0.4140" version="3.0.4140"> - <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard" value=""/> - </software> - </softwareList> - <instrumentConfigurationList count="1"> - <instrumentConfiguration id="IC"> - <cvParam cvRef="MS" accession="MS:1000031" name="instrument model" value=""/> - </instrumentConfiguration> - </instrumentConfigurationList> - <dataProcessingList count="1"> - <dataProcessing id="pwiz_Reader_conversion"> - <processingMethod order="0" softwareRef="pwiz_3.0.4140"> - <cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" value=""/> - </processingMethod> - <processingMethod order="1" softwareRef="pwiz_3.0.4140"> - <userParam name="most intense count (excluding ties at the threshold)" value="100"/> - </processingMethod> - </dataProcessing> - </dataProcessingList> - <run id="bsa" defaultInstrumentConfigurationRef="IC"> - <spectrumList count="1" defaultDataProcessingRef="pwiz_Reader_conversion"> - <spectrum index="0" id="index=0" defaultArrayLength="97" dataProcessingRef="pwiz_Reader_conversion"> - <cvParam cvRef="MS" accession="MS:1000580" name="MSn spectrum" value=""/> - <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="2"/> - <cvParam cvRef="MS" accession="MS:1000127" name="centroid spectrum" value=""/> - <cvParam cvRef="MS" accession="MS:1000796" name="spectrum title" value="Cmpd 1, +MSn(722.3522), 33.5 min"/> - <cvParam cvRef="MS" accession="MS:1000130" name="positive scan" value=""/> - <cvParam cvRef="MS" accession="MS:1000528" name="lowest observed m/z" value="198.13402"/> - <cvParam cvRef="MS" accession="MS:1000527" name="highest observed m/z" value="1280.62643"/> - 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<indexList count="2"> - <index name="spectrum"> - <offset idRef="index=0">2685</offset> - </index> - </indexList> - <indexListOffset>7058</indexListOffset> - <fileChecksum>b76171188a63cfad075d3738a172b15f1f9e0c4c</fileChecksum> -</indexedmzML> |
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| diff -r 50eb60757ca5 -r ffd1d25b8080 test-data/bsa.pepXML --- a/test-data/bsa.pepXML Sun Jun 09 08:19:31 2013 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,133 +0,0 @@\n-<?xml version="1.0" encoding="UTF-8"?>\n-<?xml-stylesheet type="text/xsl" href="pepXML_std.xsl"?>\n-<msms_pipeline_analysis xmlns="http://regis-web.systemsbiology.net/pepXML" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" date="2013:02:27:09:50:15" summary_xml="/data/galaxy/galaxy/database/job_working_directory/004/4155//data/galaxy/galaxy/database/files/004/dataset_4786.dat" xsi:schemaLocation="http://sashimi.sourceforge.net/schema_revision/pepXML/pepXML_v117.xsd">\n- <msms_run_summary base_name="/data/galaxy/galaxy/database/files/004/dataset_4783.dat" search_engine="X! Tandem (k-score)" raw_data_type="raw" raw_data="mzML">\n- <sample_enzyme name="trypsin">\n-<specificity cut="KR" no_cut="P" sense="C"/>\n-</sample_enzyme>\n-<search_summary base_name="/data/galaxy/galaxy/database/files/004/dataset_4783_tandem.tandem" search_engine="X! Tandem (k-score)" precursor_mass_type="monoisotopic" fragment_mass_type="monoisotopic" search_id="1">\n- <search_database local_path="/data/galaxy/galaxy/database/files/004/dataset_4785.dat" type="AA"/>\n- <enzymatic_search_constraint enzyme="trypsin" max_num_internal_cleavages="2" min_number_termini="1"/>\n- <aminoacid_modification aminoacid="C" massdiff="57.0215" mass="160.0306" variable="N"/>\n- <aminoacid_modification aminoacid="C" massdiff="-17.0265" mass="143.0041" variable="Y" symbol="^"/><!--X! Tandem n-terminal AA variable modification-->\n- <aminoacid_modification aminoacid="E" massdiff="-18.0106" mass="111.0320" variable="Y" symbol="^"/><!--X! Tandem n-terminal AA variable modification-->\n- <aminoacid_modification aminoacid="Q" massdiff="-17.0265" mass="111.0321" variable="Y" symbol="^"/><!--X! Tandem n-terminal AA variable modification-->\n- \n- <!-- Input parameters -->\n- <parameter name="list path, default parameters" value="/data/galaxy/tools/tpp/default/bin/isb_default_input_kscore.xml"/>\n- <parameter name="list path, taxonomy information" value="/data/galaxy/galaxy/database/files/004/dataset_4783.taxonomy.xml"/>\n- <parameter name="output, histogram column width" value="30"/>\n- <parameter name="output, histograms" value="no"/>\n- <parameter name="output, log path" value=""/>\n- <parameter name="output, maximum valid expectation value" value="0.1"/>\n- <parameter name="output, message" value="1234567890"/>\n- <parameter name="output, one sequence copy" value="no"/>\n- <parameter name="output, parameters" value="yes"/>\n- <parameter name="output, path" value="/data/galaxy/galaxy/database/files/004/dataset_4783_tandem.tandem"/>\n- <parameter name="output, path hashing" value="no"/>\n- <parameter name="output, performance" value="yes"/>\n- <parameter name="output, proteins" value="yes"/>\n- <parameter name="output, results" value="all"/>\n- <parameter name="output, sequence path" value=""/>\n- <parameter name="output, sequences" value="no"/>\n- <parameter name="output, sort results by" value="spectrum"/>\n- <parameter name="output, spectra" value="yes"/>\n- <parameter name="output, xsl path" value="tandem-style.xsl"/>\n- <parameter name="protein, C-terminal residue modification mass" value=""/>\n- <parameter name="protein, N-terminal residue modification mass" value=""/>\n- <parameter name="protein, cleavage semi" value="yes"/>\n- <parameter name="protein, cleavage site" value="[RK]|{P}"/>\n- <parameter name="protein, homolog management" value="no"/>\n- <parameter name="protein, modified residue mass file" value=""/>\n- <parameter name="protein, taxon" value="/data/galaxy/galaxy/database/files/004/dataset_4785.dat"/>\n- <parameter name="refine" value="no"/>\n- <parameter name="refine, maximum valid expectation value" value="0.1"/>\n- <parameter name="refine, sequence path" value=""/>\n- <para'..b'eads" value="1"/>\n- <parameter name="spectrum, total peaks" value="400"/>\n- <parameter name="spectrum, use conditioning" value="no"/>\n- <parameter name="spectrum, use noise suppression" value="yes"/>\n- <!-- Unused input parameters -->\n- <parameter name="refine, cleavage semi" value="yes"/>\n- <parameter name="refine, modification mass" value="57.012@C"/>\n- <parameter name="refine, point mutations" value="no"/>\n- <parameter name="refine, potential C-terminus modifications" value=""/>\n- <parameter name="refine, potential N-terminus modifications" value=""/>\n- <parameter name="refine, potential modification mass" value="15.994915@M"/>\n- <parameter name="refine, potential modification motif" value=""/>\n- <parameter name="refine, tic percent" value="10"/>\n- <parameter name="refine, unanticipated cleavage" value="no"/>\n- <parameter name="refine, use potential modifications for full refinement" value="no"/>\n- <parameter name="scoring, pluggable scoring" value="yes"/>\n- <!-- Performance parameters -->\n- <parameter name="list path, sequence source #1" value="/data/galaxy/galaxy/database/files/004/dataset_4785.dat"/>\n- <parameter name="list path, sequence source description #1" value="no description"/>\n- <parameter name="modelling, spectrum noise suppression ratio" value="0.00"/>\n- <parameter name="modelling, total peptides used" value="1"/>\n- <parameter name="modelling, total proteins used" value="2"/>\n- <parameter name="modelling, total spectra used" value="1"/>\n- <parameter name="process, start time" value="2013:02:27:09:50:15"/>\n- <parameter name="process, version" value="x! tandem 2010.10.01.1 (LabKey, Insilicos and ISB)"/>\n- <parameter name="quality values" value="0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0"/>\n- <parameter name="refining, # input models" value="0"/>\n- <parameter name="refining, # input spectra" value="0"/>\n- <parameter name="refining, # partial cleavage" value="0"/>\n- <parameter name="refining, # point mutations" value="0"/>\n- <parameter name="refining, # potential C-terminii" value="0"/>\n- <parameter name="refining, # potential N-terminii" value="0"/>\n- <parameter name="refining, # unanticipated cleavage" value="0"/>\n- <parameter name="timing, initial modelling total (sec)" value="0.00"/>\n- <parameter name="timing, initial modelling/spectrum (sec)" value="0.000"/>\n- <parameter name="timing, load sequence models (sec)" value="0.00"/>\n- <parameter name="timing, refinement/spectrum (sec)" value="0.000"/>\n- </search_summary>\n- \n- <spectrum_query spectrum="dataset_4783.dat.00000.00000.2" start_scan="0" end_scan="0" precursor_neutral_mass="1442.6899" assumed_charge="2" index="1">\n- <search_result>\n- <search_hit hit_rank="1" peptide="YICDNQDTISSK" peptide_prev_aa="K" peptide_next_aa="L" protein="sp|ALBU_BOVIN|" num_tot_proteins="1" num_matched_ions="14" tot_num_ions="22" calc_neutral_pep_mass="1442.6347" massdiff="0.055" num_tol_term="2" num_missed_cleavages="0" is_rejected="0">\n- <modification_info>\n- <mod_aminoacid_mass position="3" mass="160.0306"/>\n- </modification_info>\n- <search_score name="hyperscore" value="491"/>\n- <search_score name="nextscore" value="287"/>\n- <search_score name="bscore" value="0"/>\n- <search_score name="yscore" value="2"/>\n- <search_score name="cscore" value="0"/>\n- <search_score name="zscore" value="0"/>\n- <search_score name="ascore" value="0"/>\n- <search_score name="xscore" value="0"/>\n- <search_score name="expect" value="0.12"/>\n- </search_hit>\n- </search_result>\n- </spectrum_query>\n- </msms_run_summary>\n-</msms_pipeline_analysis>\n' |
| b |
| diff -r 50eb60757ca5 -r ffd1d25b8080 tool-data/pepxml_databases.loc.sample --- a/tool-data/pepxml_databases.loc.sample Sun Jun 09 08:19:31 2013 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -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_ |
| b |
| diff -r 50eb60757ca5 -r ffd1d25b8080 tool-data/tandem_mods.loc.sample --- a/tool-data/tandem_mods.loc.sample Sun Jun 09 08:19:31 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 |
| b |
| diff -r 50eb60757ca5 -r ffd1d25b8080 tool_dependencies.xml --- a/tool_dependencies.xml Sun Jun 09 08:19:31 2013 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,10 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="galaxy_protk" version="1.2.2"> - <repository toolshed="http://toolshed.g2.bx.psu.edu" name="galaxy_protk" owner="iracooke" changeset_revision="c25df71f7b68" prior_installation_required="True"/> - </package> - - <package name="trans_proteomic_pipeline" version="4.6.1"> - <repository toolshed="http://toolshed.g2.bx.psu.edu" name="protk_trans_proteomic_pipeline" owner="iracooke" changeset_revision="e85a18371516"/> - </package> -</tool_dependency> |