| Previous changeset 10:ffd1d25b8080 (2014-06-16) Next changeset 12:f9271f6991b1 (2014-06-16) |
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Commit message:
Uploaded |
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added:
README repository_dependencies.xml tandem.xml tool-data/pepxml_databases.loc.sample tool-data/tandem_mods.loc.sample |
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removed:
README.md tandem_to_pepxml.xml |
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| diff -r ffd1d25b8080 -r 618d74240c7f README --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README Mon Jun 16 05:47:55 2014 -0400 |
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| @@ -0,0 +1,6 @@ +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 |
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| diff -r ffd1d25b8080 -r 618d74240c7f README.md --- a/README.md Mon Jun 16 05:47:38 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,6 +0,0 @@ -## 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 ffd1d25b8080 -r 618d74240c7f repository_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/repository_dependencies.xml Mon Jun 16 05:47:55 2014 -0400 |
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| @@ -0,0 +1,4 @@ +<?xml version="1.0"?> +<repositories description="Proteomics datatypes"> + <repository changeset_revision="f66f8ca7b7b9" name="proteomics_datatypes" owner="iracooke" toolshed="http://toolshed.g2.bx.psu.edu" /> + </repositories> |
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| diff -r ffd1d25b8080 -r 618d74240c7f tandem.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tandem.xml Mon Jun 16 05:47:55 2014 -0400 |
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| b'@@ -0,0 +1,204 @@\n+<tool id="proteomics_search_tandem_1" name="X!Tandem MSMS Search" version="1.0.2">\n+\n+ <requirements>\n+\t <requirement type="package" version="1.3.0">protk</requirement>\n+ </requirements>\n+\n+\t<description>Run an X!Tandem Search</description>\n+\n+\t<command>\n+\t\t#if $database.source_select=="built_in":\n+\t\ttandem_search.rb -d $database.dbkey \n+\t\t#else \n+\t\ttandem_search.rb -d $database.fasta_file\n+\t\t#end if\n+\n+\t\t#if $tandem_params.source_select=="built_in":\n+\t\t-T $tandem_params.paramskey \n+\t\t#else \n+\t\t-T $tandem_params.params_file\n+\t\t#end if\n+\n+\n+\t\t--var-mods=\'\n+\t\t$variable_mods\n+\t\t#for $custom_variable_mod in $custom_variable_mods:\n+\t\t,${custom_variable_mod.custom_mod}\n+\t\t#end for\n+\t\t\'\n+\n+\t\t--fix-mods=\'\n+\t\t$fixed_mods\n+\t\t#for $custom_fix_mod in $custom_fix_mods:\n+\t\t,${custom_fix_mod.custom_mod}\n+\t\t#end for\n+\t\t\'\n+\n+\t\t$input_file -o $output -r \n+\n+\t\t--enzyme=$enzyme \n+\n+\t\t--precursor-ion-tol-units=$precursor_tolu \n+\n+\t\t-v $missed_cleavages \n+\n+\t\t-f $fragment_ion_tol \n+\n+\t\t-p $precursor_ion_tol \n+\n+\t\t$allow_multi_isotope_search \n+\n+\t\t$acetyl_protein_nterm\n+\n+\t\t$cleavage_semi\n+\n+\t\t$keep_spectra\n+\n+\t\t--threads $threads\n+\t\t\n+\t</command>\n+\n+\t<inputs>\n+\t\t<conditional name="database">\n+\t\t\t<param name="source_select" type="select" label="Database source">\n+\t\t\t\t<option value="built_in">Built-In</option>\n+\t\t\t\t<option value="input_ref" selected="true">Your Upload File</option>\n+\t\t\t</param>\n+\t\t\t<when value="built_in">\n+\t\t\t\t<param name="dbkey" type="select" format="text" >\n+\t\t\t\t\t<label>Database</label>\n+\t\t\t\t\t<options from_file="pepxml_databases.loc">\n+\t\t\t\t\t\t<column name="name" index="0" />\n+\t\t\t\t\t\t<column name="value" index="2" />\n+\t\t\t\t\t</options>\n+\t\t\t\t</param>\n+\t\t\t</when>\n+\t\t\t<when value="input_ref">\n+\t\t\t\t<param name="fasta_file" type="data" format="fasta" label="Uploaded FASTA file" />\n+\t\t\t</when>\n+\t\t</conditional>\n+\t\t\n+\t\t<conditional name="tandem_params">\n+\t\t\t<param name="source_select" type="select" label="Baseline Parameters">\n+\t\t\t\t<option value="built_in" selected="true">Built-In</option>\n+\t\t\t\t<option value="input_ref">Custom parameter file</option>\n+\t\t\t</param>\n+\t\t\t<when value="built_in">\n+\t\t\t\t<param name="paramskey" type="select" format="text" >\n+\t\t\t\t\t<label>Paramset</label>\n+\t\t\t\t <option value="isb_native">ISB Native</option>\t\t\n+\t\t\t\t\t<option value="isb_kscore">ISB K-Score</option>\n+\t\t\t\t</param>\n+\t\t\t</when>\n+\t\t\t<when value="input_ref">\n+\t\t\t\t<param name="params_file" type="data" format="xml" label="Custom X!Tandem Parameters" />\n+\t\t\t</when>\n+\t\t</conditional>\n+\n+\t\t<param name="input_file" type="data" format="mzml,mgf" multiple="false" label="MSMS File" help="A file with MS/MS data"/>\n+\n+\t\t<param name="variable_mods" format="text" type="select" multiple="true" label="Variable Modifications" help="Hold the appropriate key while\n+\t\t\tclicking to select multiple items">\n+\t\t\t<options from_file="tandem_mods.loc">\n+\t\t\t\t<column name="name" index="0" />\n+\t\t\t\t<column name="value" index="2" />\n+\t\t\t</options>\n+\t\t</param>\n+\n+\t\t<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).">\n+\t\t\t<param name="custom_mod" type="text">\n+\t\t\t</param>\n+\t\t</repeat>\n+\t\t\n+\t\t\n+\t\t<param name="fixed_mods" format="text" type="select" multiple="true" label="Fixed Modifications" help="Hold the appropriate key while\n+\t\t\tclicking to select multiple items">\n+\t\t\t<options from_file="tandem_mods.loc">\n+\t\t\t\t<column name="name" index="0" />\n+\t\t\t\t<column name="value" index="2" />\n+\t\t\t</options>\n+\t\t</param>\n+\n+\t\t<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).">\n+\t\t\t<param name="custom_mod" type="text">\n+\t\t\t</param>\n+\t\t</repeat>\n+\n+\t\t<par'..b'nal protein acetylation as a variable modification" truevalue="-y" falsevalue="" />\t\t\n+\t\t\n+\n+\t\t<param name="missed_cleavages" type="select" format="text" help="Allow peptides to contain up to this many missed enzyme cleavage sites">\n+\t\t\t<label>Missed Cleavages Allowed</label>\n+\t\t <option value="0">0</option>\t\t\n+\t\t\t<option value="1">1</option>\n+\t\t\t<option value="2">2</option>\n+\t\t</param>\n+\n+\t\t<param name="cleavage_semi" type="boolean" label="Allow semi-cleaved peptides" help="This can increase search time dramatically" truevalue="--cleavage-semi" falsevalue=""/>\n+\n+\t\t<param name="keep_spectra" type="boolean" label="Keep Spectra" help="Include spectra in the output" truevalue="--output-spectra" falsevalue=""/>\n+\n+\t\t<param name="threads" type="integer" value="1" label="Threads" help="Number of threads to use for search. Maximum is 16"/>\n+\t\t\n+\t\t<param name="enzyme" type="select" format="text">\n+\t\t <label>Enzyme</label>\n+\t\t\t<option value="[R]|{P}">argc - [R]|{P}</option>\n+\t\t\t<option value="[X]|[D]">aspn - [X]|[D]</option>\n+\t\t\t<option value="[FLMWY]|{P}">chymotrypsin - [FLMWY]|{P}</option>\n+\t\t\t<option value="[R]|[X]">clostripain - [R]|[X]</option>\n+\t\t\t<option value="[M]|{P}">cnbr - [M]|{P}</option>\n+\t\t\t<option value="[AGILV]|{P}">elastase - [AGILV]|{P}</option>\n+\t\t\t<option value="[D]|{P}">formicacid - [D]|{P}</option>\n+\t\t\t<option value="[DE]|{P}">gluc - [DE]|{P}</option>\n+\t\t\t<option value="[E]|{P}">gluc_bicarb - [E]|{P}</option>\n+\t\t\t<option value="[W]|[X]">iodosobenzoate - [W]|[X]</option>\n+\t\t\t<option value="[K]|{P}">lysc - [K]|{P}</option>\n+\t\t\t<option value="[K]|[X]">lysc-p - [K]|[X]</option>\n+\t\t\t<option value="[X]|[K]">lysn - [X]|[K]</option>\n+\t\t\t<option value="[X]|[AKRS]">lysn_promisc - [X]|[AKRS]</option>\n+\t\t\t<option value="[X]|[X]">nonspecific - [X]|[X]</option>\n+\t\t\t<option value="[FL]|[X]">pepsina - [FL]|[X]</option>\n+\t\t\t<option value="[P]|[X]">protein_endopeptidase - [P]|[X]</option>\n+\t\t\t<option value="[E]|[X]">staph_protease - [E]|[X]</option>\n+\t\t\t<option value="[FMWY]|{P},[KR]|{P},[X]|[D]">tca - [FMWY]|{P},[KR]|{P},[X]|[D]</option>\n+\t\t\t<option value="[KR]|{P}" selected="true">trypsin - [KR]|{P}</option>\n+\t\t\t<option value="[FKLMRWY]|{P}">trypsin/chymotrypsin - [FKLMRWY]|{P}</option>\n+\t\t\t<option value="[KR]|{P},[M]|{P}">trypsin/cnbr - [KR]|{P},[M]|{P}</option>\n+\t\t\t<option value="[DEKR]|{P}">trypsin_gluc - [DEKR]|{P}</option>\n+\t\t</param>\n+\n+\t\t\n+\t\t<param name="fragment_ion_tol" help="Fragment Ion Tolerance in Daltons" type="float" value="0.65" min="0" max="10000" label="Fragment ion tolerance"/>\n+\n+\t\t<param name="precursor_ion_tol" help="Precursor Ion Tolerance (Da or ppm)" type="float" value="100" min="0" max="10000" label="Precursor ion tolerance"/>\n+\t\t<param name="precursor_tolu" type="select" format="text">\n+\t\t <label>Precursor Ion Tolerance Units</label>\n+\t\t <option value="ppm">ppm</option>\t\t\n+\t\t\t<option value="Da">Da</option>\n+\t\t</param>\n+\t\t\n+\t\t<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=""/>\n+\n+\t</inputs>\n+\n+\n+\t<outputs>\n+\t\t<data format="tandem" 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}.tandem"/>\n+\t</outputs>\n+\n+\n+ <help>\n+\n+**What it does**\n+\n+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.\n+\n+----\n+\n+**References**\n+\n+Please see http://www.thegpm.org/GPM/references.html for details of references describing the X!Tandem search engine.\n+\n+ </help>\n+\n+</tool>\n' |
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| diff -r ffd1d25b8080 -r 618d74240c7f tandem_to_pepxml.xml --- a/tandem_to_pepxml.xml Mon Jun 16 05:47:38 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,25 +0,0 @@ -<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 ffd1d25b8080 -r 618d74240c7f tool-data/pepxml_databases.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/pepxml_databases.loc.sample Mon Jun 16 05:47:55 2014 -0400 |
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| @@ -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_ |
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| diff -r ffd1d25b8080 -r 618d74240c7f tool-data/tandem_mods.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/tandem_mods.loc.sample Mon Jun 16 05:47:55 2014 -0400 |
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| @@ -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 |