| Next changeset 1:7a74818e0eeb (2013-06-20) |
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Initial commit. |
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added:
LICENSE README.md README_GALAXYP.md README_REPO.md build_mods_loc.py peptide_shaker.xml searchGUI_mods.xml searchGUI_usermods.xml searchgui_mods.loc searchgui_mods.loc.sample update.sh |
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| diff -r 000000000000 -r 0578e296cab4 LICENSE --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/LICENSE Fri May 10 17:58:22 2013 -0400 |
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| @@ -0,0 +1,11 @@ +--2012-09-19 08:46:18-- http://www.apache.org/licenses/LICENSE-2.0.txt +Resolving www.apache.org... 140.211.11.131, 192.87.106.229, 2001:610:1:80bc:192:87:106:229 +Connecting to www.apache.org|140.211.11.131|:80... connected. +HTTP request sent, awaiting response... 200 OK +Length: 11358 (11K) [text/plain] +Saving to: “LICENSE-2.0.txt” + + 0K .......... . 100% 200K=0.06s + +2012-09-19 08:46:18 (200 KB/s) - “LICENSE-2.0.txt” saved [11358/11358] + |
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| diff -r 000000000000 -r 0578e296cab4 README.md --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.md Fri May 10 17:58:22 2013 -0400 |
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| @@ -0,0 +1,40 @@ +Tool wrapper for SearchGUI + PeptideShaker. This tool takes any number +of mgf files and performs X! Tandem and OMSSA searches on these via +SearchGUI and merges the results using PeptideShaker. + +For Galaxy-P we are installing this tool via CloudBioLinux +(https://github.com/jmchilton/cloudbiolinux/blob/proteomics/cloudbio/custom/bio_proteomics.py). While +this fabric script may not be exactly appropriate for your environment +it may serve as a template for how to install this software. In +particular these tools require CLI wrappers to be placed for +PeptideShaker and SearchGUI that can be installed as demostrated in +these fabric functions. + +Note: Also SearchGUI requires a version greater than 1.12.2 which +contained several bugs preventing this from working on the +command-line and via Linux. + +Also, PeptideShaker may require xvfb to simulate an X environment if +this is installed on a headless server. +# Obtaining Tools + +Repositories for all Galaxy-P tools can be found at +https:/bitbucket.org/galaxyp/. + +# Contact + +Please send suggestions for improvements and bug reports to +jmchilton@gmail.com. + +# License + +All Galaxy-P tools are licensed under the Apache License Version 2.0 +unless otherwise documented. + +# Tool Versioning + +Galaxy-P tools will have versions of the form X.Y.Z. Versions +differing only after the second decimal should be completely +compatible with each other. Breaking changes should result in an +increment of the number before and/or after the first decimal. All +tools of version less than 1.0.0 should be considered beta. |
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| diff -r 000000000000 -r 0578e296cab4 README_GALAXYP.md --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README_GALAXYP.md Fri May 10 17:58:22 2013 -0400 |
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| @@ -0,0 +1,22 @@ +# Obtaining Tools + +Repositories for all Galaxy-P tools can be found at +https:/bitbucket.org/galaxyp/. + +# Contact + +Please send suggestions for improvements and bug reports to +jmchilton@gmail.com. + +# License + +All Galaxy-P tools are licensed under the Apache License Version 2.0 +unless otherwise documented. + +# Tool Versioning + +Galaxy-P tools will have versions of the form X.Y.Z. Versions +differing only after the second decimal should be completely +compatible with each other. Breaking changes should result in an +increment of the number before and/or after the first decimal. All +tools of version less than 1.0.0 should be considered beta. |
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| diff -r 000000000000 -r 0578e296cab4 README_REPO.md --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README_REPO.md Fri May 10 17:58:22 2013 -0400 |
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| @@ -0,0 +1,18 @@ +Tool wrapper for SearchGUI + PeptideShaker. This tool takes any number +of mgf files and performs X! Tandem and OMSSA searches on these via +SearchGUI and merges the results using PeptideShaker. + +For Galaxy-P we are installing this tool via CloudBioLinux +(https://github.com/jmchilton/cloudbiolinux/blob/proteomics/cloudbio/custom/bio_proteomics.py). While +this fabric script may not be exactly appropriate for your environment +it may serve as a template for how to install this software. In +particular these tools require CLI wrappers to be placed for +PeptideShaker and SearchGUI that can be installed as demostrated in +these fabric functions. + +Note: Also SearchGUI requires a version greater than 1.12.2 which +contained several bugs preventing this from working on the +command-line and via Linux. + +Also, PeptideShaker may require xvfb to simulate an X environment if +this is installed on a headless server. |
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| diff -r 000000000000 -r 0578e296cab4 build_mods_loc.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/build_mods_loc.py Fri May 10 17:58:22 2013 -0400 |
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| @@ -0,0 +1,12 @@ +#!/usr/bin/env python + +import xml.etree.ElementTree as ET +from os.path import exists + +with open("searchgui_mods.loc", "w") as output: + for mods_path in ["searchGUI_mods.xml", "searchGUI_usermods.xml"]: + tree = ET.parse(mods_path) + modifications_el = tree.getroot() + for mod in modifications_el.findall("{http://www.ncbi.nlm.nih.gov}MSModSpec"): + name_el = mod.find("{http://www.ncbi.nlm.nih.gov}MSModSpec_name") + output.write("%s\n" % name_el.text.lower()) |
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| diff -r 000000000000 -r 0578e296cab4 peptide_shaker.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/peptide_shaker.xml Fri May 10 17:58:22 2013 -0400 |
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| b'@@ -0,0 +1,221 @@\n+<tool id="peptide_shaker" name="Peptide Shaker" version="0.1.0">\n+ <!-- TODO: Set defaults for weights correctly -->\n+ <description>\n+ Peform protein identification combining X! Tandem and OMSSA (using SearchGUI) and PeptideShaker pipeline.\n+ </description>\n+ <command>\n+ mkdir spectra;\n+ mkdir output;\n+ mkdir output_reports;\n+ cwd=`pwd`;\n+ #for $mgf in $peak_lists:\n+ #set $input_name = $mgf.display_name.replace(".mgf", "") + ".mgf"\n+ ln -s \'$mgf\' \'spectra/$input_name\';\n+ #end for\n+ SearchCLI \\\n+ -spectrum_files \\$cwd/spectra \\\n+ -output_folder \\$cwd/output \\\n+ -ppm $precursor_ion_tol_units \\\n+ -prec_tol $precursor_ion_tol \\\n+ -frag_tol $fragment_tol \\\n+ -enzyme \'$enzyme\' \\\n+ #set $fixed_mods_str = $fixed_modifications or \'\'\n+ #set $variable_mods_str = $variable_modifications or \'\'\n+ #if $fixed_mods_str\n+ -fixed_mods "$fixed_mods_str" \\\n+ #end if\n+ #if $variable_mods_str\n+ -variable_mods "$variable_mods_str" \\\n+ #end if\n+ -mc $missed_cleavages \\\n+ #if $advanced.specify:\n+ -xtandem $advanced.xtandem \\\n+ #if $advanced.omssa.run_omssa\n+ #set $omssa = 1\n+ #else \n+ #set $omssa = 0\n+ #end if\n+ -omssa $omssa \\\n+ #if $omssa == 1\n+ -hitlist_length ${advanced.omssa.hitlist_length} \\\n+ -remove_prec ${advanced.omssa.remove_precursor} \\\n+ -scale_prec ${advanced.omssa.scale_precursor} \\\n+ -estimate_charge ${advanced.omssa.estimate_charge} \\\n+ #end if\n+ #end if\n+ -db $input_database;\n+ PeptideShakerCLI \\\n+ -experiment \'Galaxy Experiment\' \\\n+ -sample \'Sample\' \\ \n+ -replicate 1 \\\n+ -spectrum_files \\$cwd/spectra \\\n+ -identification_files \\$cwd/output \\ \n+ -search_params \\$cwd/output/SearchGUI.parameters \\\n+ -out_txt_1 \\$cwd/output_reports \\\n+ #if $processing_options.specify\n+ -protein_FDR ${processing_options.protein_fdr} \\\n+ -peptide_FDR ${processing_options.peptide_fdr} \\ \n+ -psm_FDR ${processing_options.psm_fdr} \\\n+ -psm_FLR ${processing_options.psm_flr} \\\n+ #if str($processing_options.a_score.use) == "1"\n+ #set $a_score = 1\n+ #else\n+ #set $a_score = 0\n+ #end if\n+ -a_score $a_score \\\n+ #if str($a_score) == "1"\n+ -a_score_neutral_losses ${processing_options.a_score.neutral_losses} \\\n+ #end if\n+ #end if\n+ #if $filtering_options.specify\n+ -min_peptide_length ${filtering_options.min_peptide_length} \\\n+ -max_peptide_length ${filtering_options.max_peptide_length} \\\n+ -max_precursor_error ${filtering_options.max_precursor_error} \\\n+ -max_precursor_error_type ${filtering_options.max_precursor_error_type} \\\n+ -max_xtandem_e ${filtering_options.max_xtandem_e} \\\n+ -max_omssa_e ${filtering_options.max_omssa_e} \\\n+ -exclude_unknown_ptms ${filtering_options.exclude_unknown_ptms} \\\n+ #end if\n+ -out \\$cwd/output.cps ; \n+ mv output_reports/*peptides.txt peptides.txt ;\n+ mv output_reports/*psms.txt psms.txt ;\n+ mv output_reports/*proteins.txt proteins.txt\n+ </command>\n+ <stdio>\n+ <exit_code range="1:" level="fatal" description="Job Failed" />\n+ </stdio>\n+ <inputs>\n+ <param format="fasta" name="input_database" type="data" label="Protein Database"/>\n+ <param format="mgf" name="peak_lists" type="data" multiple="true" label="Input Peak Lists (mgf)" />\n+ <param name="precursor_ion_tol_units" type="select" label="Precursor Ion Tolerance Units">\n+ <option value="1">Parts per million (ppm)</option>\n+ <option value="0">Daltons</option>\n+ </param> \n+ <param name="precursor_ion_tol" type="float" value="10" label="Percursor Ion Tolerance" />\n+ <param name="fragment_tol" type="float" value="0.5" label="Fragment Tolerance (Daltons)" />\n+ <param name="enzyme" type="select" label="Enzyme">\n+ <option value="Trypsin">Trypsin</option>\n+ <option value="Arg-C">Arg-C</option>\n+ <option value="CNBr">CNBr</option>\n+ <option value="Chymotrypsin (FYWL)">Chymotrypsin (FYWL)<'..b't List Length" type="integer" value="25" />\n+ <param name="remove_precursor" label="OMSSA: Remove Precurosr" type="boolean" truevalue="1" falsevalue="0" checked="true"/>\n+ <param name="scale_precursor" label="OMSSA: Scale Precursor Mass" type="boolean" truevalue="1" falsevalue="0" checked="false"/>\n+ <param name="estimate_charge" label="OMSSA: Estimate Charge" type="boolean" truevalue="1" falsevalue="0" checked="true" />\n+ </when>\n+ </conditional>\n+ </when>\n+ </conditional>\n+ <conditional name="processing_options">\n+ <param name="specify" label="Specify Advanced PeptideShaker Processing Options" type="boolean" truevalue="true" falsevalue="false" />\n+ <when value="false" />\n+ <when value="true">\n+ <param name="protein_fdr" label="FDR at the protein level" help="In percent (default 1% FDR: \'1\')" value="1" type="float" />\n+ <param name="peptide_fdr" label="FDR at the peptide level" help="In percent (default 1% FDR: \'1\')" value="1" type="float" />\n+ <param name="psm_fdr" label="FDR at the PSM level" help="In percent (default 1% FDR: \'1\')" value="1" type="float" />\n+ <param name="psm_flr" label="FLR at the PSM level" help="In percent (default 1% FLR: \'1\'). Percent for peptides with different potential modification sites and one variable modification." value="1" type="float" />\n+ <conditional name="a_score">\n+ <param name="use" label="Calculate A Score" type="boolean" truevalue="1" falsevalue="0" checked="true" />\n+ <when value="0" />\n+ <when value="1">\n+ <param name="neutral_losses" label="Include Neutral Losses in A Score" type="boolean" truevalue="1" falsevalue="0" />\n+ </when>\n+ </conditional>\n+ <!-- SKIPPING -protein_fraction_mw_confidence ${processing_options.protein_fraction_mw_confidence} -->\n+ </when>\n+ </conditional> \n+ <conditional name="filtering_options">\n+ <param name="specify" label="Specify Advanced PeptideShaker Filtering Options" type="boolean" truevalue="true" falsevalue="false" />\n+ <when value="false" />\n+ <when value="true">\n+ <param name="min_peptide_length" label="Minimum Peptide Length" value="6" type="integer" />\n+ <param name="max_peptide_length" label="Maximum Peptide Length" value="30" type="integer" />\n+ <param name="max_precursor_error" label="Maximum Precursor Error" value="10" type="float" help="Next option specifies units (Da or ppm)." />\n+ <param name="max_precursor_error_type" label="Maximum Precursor Error Type" type="select">\n+ <option value="0">ppm</option>\n+ <option value="1">Daltons</option>\n+ </param>\n+ <param name="max_xtandem_e" label="Maximum X! Tandem E Value" value="100" type="float" help="" />\n+ <param name="max_omssa_e" label="Maximum OMSSA E Value" value="100" type="float" help="" />\n+ <param name="exclude_unknown_ptms" label="Exclude Unknown PTMs" type="boolean" truevalue="1" falsevalue="0" checked="true" />\n+ </when>\n+ </conditional>\n+ </inputs>\n+ <outputs>\n+ <data format="cps" name="output" label="PeptideShaker CPS results for ${on_string}" from_work_dir="output.cps" />\n+ <data format="tabular" name="output_peptides" label="PeptideShaker Peptide Report for ${on_string}" from_work_dir="peptides.txt" />\n+ <data format="tabular" name="output_proteins" label="PeptideShaker Protein Report for ${on_string}" from_work_dir="proteins.txt" />\n+ <data format="tabular" name="output_psms" label="PeptideShaker PSM Report for ${on_string}" from_work_dir="psms.txt" />\n+ </outputs>\n+ <requirements>\n+ <requirement type="package">peptide_shaker</requirement>\n+ <requirement type="package">searchgui</requirement>\n+ </requirements>\n+ <help>\n+**What it does**\n+\n+------\n+\n+**Citation**\n+\n+For the underlying tool, please cite `TODO`\n+\n+If you use this tool in Galaxy, please cite TODO\n+ </help>\n+</tool>\n' |
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| diff -r 000000000000 -r 0578e296cab4 searchGUI_mods.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/searchGUI_mods.xml Fri May 10 17:58:22 2013 -0400 |
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| b'@@ -0,0 +1,3021 @@\n+<?xml version="1.0"?>\n+<MSModSpecSet\n+ xmlns="http://www.ncbi.nlm.nih.gov"\n+ xmlns:xs="http://www.w3.org/2001/XMLSchema-instance"\n+ xs:schemaLocation="http://www.ncbi.nlm.nih.gov OMSSA.xsd"\n+ >\n+ <MSModSpec>\n+ <MSModSpec_mod>\n+ <MSMod value="methylk">0</MSMod>\n+ </MSModSpec_mod>\n+ <MSModSpec_type>\n+ <MSModType value="modaa">0</MSModType>\n+ </MSModSpec_type>\n+ <MSModSpec_name>methylation of K</MSModSpec_name>\n+ <MSModSpec_monomass>14.015650</MSModSpec_monomass>\n+ <MSModSpec_averagemass>14.0266</MSModSpec_averagemass>\n+ <MSModSpec_n15mass>0</MSModSpec_n15mass>\n+ <MSModSpec_residues>\n+ <MSModSpec_residues_E>K</MSModSpec_residues_E>\n+ </MSModSpec_residues>\n+ <MSModSpec_unimod>34</MSModSpec_unimod>\n+ <MSModSpec_psi-ms>Methyl</MSModSpec_psi-ms>\n+ </MSModSpec>\n+ <MSModSpec>\n+ <MSModSpec_mod>\n+ <MSMod value="oxym">1</MSMod>\n+ </MSModSpec_mod>\n+ <MSModSpec_type>\n+ <MSModType value="modaa">0</MSModType>\n+ </MSModSpec_type>\n+ <MSModSpec_name>oxidation of M</MSModSpec_name>\n+ <MSModSpec_monomass>15.994915</MSModSpec_monomass>\n+ <MSModSpec_averagemass>15.9994</MSModSpec_averagemass>\n+ <MSModSpec_n15mass>0</MSModSpec_n15mass>\n+ <MSModSpec_residues>\n+ <MSModSpec_residues_E>M</MSModSpec_residues_E>\n+ </MSModSpec_residues>\n+ <MSModSpec_unimod>35</MSModSpec_unimod>\n+ <MSModSpec_psi-ms>Oxidation</MSModSpec_psi-ms>\n+ </MSModSpec>\n+ <MSModSpec>\n+ <MSModSpec_mod>\n+ <MSMod value="carboxymethylc">2</MSMod>\n+ </MSModSpec_mod>\n+ <MSModSpec_type>\n+ <MSModType value="modaa">0</MSModType>\n+ </MSModSpec_type>\n+ <MSModSpec_name>carboxymethyl C</MSModSpec_name>\n+ <MSModSpec_monomass>58.005479</MSModSpec_monomass>\n+ <MSModSpec_averagemass>58.0361</MSModSpec_averagemass>\n+ <MSModSpec_n15mass>0</MSModSpec_n15mass>\n+ <MSModSpec_residues>\n+ <MSModSpec_residues_E>C</MSModSpec_residues_E>\n+ </MSModSpec_residues>\n+ <MSModSpec_unimod>6</MSModSpec_unimod>\n+ <MSModSpec_psi-ms>Carboxymethyl</MSModSpec_psi-ms>\n+ </MSModSpec>\n+ <MSModSpec>\n+ <MSModSpec_mod>\n+ <MSMod value="carbamidomethylc">3</MSMod>\n+ </MSModSpec_mod>\n+ <MSModSpec_type>\n+ <MSModType value="modaa">0</MSModType>\n+ </MSModSpec_type>\n+ <MSModSpec_name>carbamidomethyl C</MSModSpec_name>\n+ <MSModSpec_monomass>57.021464</MSModSpec_monomass>\n+ <MSModSpec_averagemass>57.0513</MSModSpec_averagemass>\n+ <MSModSpec_n15mass>0</MSModSpec_n15mass>\n+ <MSModSpec_residues>\n+ <MSModSpec_residues_E>C</MSModSpec_residues_E>\n+ </MSModSpec_residues>\n+ <MSModSpec_unimod>4</MSModSpec_unimod>\n+ <MSModSpec_psi-ms>Carbamidomethyl</MSModSpec_psi-ms>\n+ </MSModSpec>\n+ <MSModSpec>\n+ <MSModSpec_mod>\n+ <MSMod value="deamidationkq">4</MSMod>\n+ </MSModSpec_mod>\n+ <MSModSpec_type>\n+ <MSModType value="modaa">0</MSModType>\n+ </MSModSpec_type>\n+ <MSModSpec_name>deamidation of N and Q</MSModSpec_name>\n+ <MSModSpec_monomass>0.984016</MSModSpec_monomass>\n+ <MSModSpec_averagemass>0.9848</MSModSpec_averagemass>\n+ <MSModSpec_n15mass>0</MSModSpec_n15mass>\n+ <MSModSpec_residues>\n+ <MSModSpec_residues_E>N</MSModSpec_residues_E>\n+ <MSModSpec_residues_E>Q</MSModSpec_residues_E>\n+ </MSModSpec_residues>\n+ <MSModSpec_unimod>7</MSModSpec_unimod>\n+ <MSModSpec_psi-ms>Deamidated</MSModSpec_psi-ms>\n+ </MSModSpec>\n+ <MSModSpec>\n+ <MSModSpec_mod>\n+ <MSMod value="propionamidec">5</MSMod>\n+ </MSModSpec_mod>\n+ <MSModSpec_type>\n+ <MSModType value="modaa">0</MSMo'..b'dSpec_n15mass>0</MSModSpec_n15mass>\n+ <MSModSpec_residues>\n+ <MSModSpec_residues_E>K</MSModSpec_residues_E>\n+ </MSModSpec_residues>\n+ <MSModSpec_unimod>730</MSModSpec_unimod>\n+ </MSModSpec>\n+ <MSModSpec>\n+ <MSModSpec_mod>\n+ <MSMod value="mod202">202</MSMod>\n+ </MSModSpec_mod>\n+ <MSModSpec_type>\n+ <MSModType value="modaa">0</MSModType>\n+ </MSModSpec_type>\n+ <MSModSpec_name>iTRAQ8plex:13C(7)15N(1) on Y</MSModSpec_name>\n+ <MSModSpec_monomass>304.205360</MSModSpec_monomass>\n+ <MSModSpec_averagemass>304.3074</MSModSpec_averagemass>\n+ <MSModSpec_n15mass>0</MSModSpec_n15mass>\n+ <MSModSpec_residues>\n+ <MSModSpec_residues_E>Y</MSModSpec_residues_E>\n+ </MSModSpec_residues>\n+ <MSModSpec_unimod>730</MSModSpec_unimod>\n+ </MSModSpec>\n+ <MSModSpec>\n+ <MSModSpec_mod>\n+ <MSMod value="mod203">203</MSMod>\n+ </MSModSpec_mod>\n+ <MSModSpec_type>\n+ <MSModType value="modnp">5</MSModType>\n+ </MSModSpec_type>\n+ <MSModSpec_name>iTRAQ8plex:13C(6)15N(2) on nterm</MSModSpec_name>\n+ <MSModSpec_monomass>304.199040</MSModSpec_monomass>\n+ <MSModSpec_averagemass>304.3081</MSModSpec_averagemass>\n+ <MSModSpec_n15mass>0</MSModSpec_n15mass>\n+ <MSModSpec_unimod>731</MSModSpec_unimod>\n+ </MSModSpec>\n+ <MSModSpec>\n+ <MSModSpec_mod>\n+ <MSMod value="mod204">204</MSMod>\n+ </MSModSpec_mod>\n+ <MSModSpec_type>\n+ <MSModType value="modaa">0</MSModType>\n+ </MSModSpec_type>\n+ <MSModSpec_name>iTRAQ8plex:13C(6)15N(2) on K</MSModSpec_name>\n+ <MSModSpec_monomass>304.199040</MSModSpec_monomass>\n+ <MSModSpec_averagemass>304.3081</MSModSpec_averagemass>\n+ <MSModSpec_n15mass>0</MSModSpec_n15mass>\n+ <MSModSpec_residues>\n+ <MSModSpec_residues_E>K</MSModSpec_residues_E>\n+ </MSModSpec_residues>\n+ <MSModSpec_unimod>731</MSModSpec_unimod>\n+ </MSModSpec>\n+ <MSModSpec>\n+ <MSModSpec_mod>\n+ <MSMod value="mod205">205</MSMod>\n+ </MSModSpec_mod>\n+ <MSModSpec_type>\n+ <MSModType value="modaa">0</MSModType>\n+ </MSModSpec_type>\n+ <MSModSpec_name>iTRAQ8plex:13C(6)15N(2) on Y</MSModSpec_name>\n+ <MSModSpec_monomass>304.199040</MSModSpec_monomass>\n+ <MSModSpec_averagemass>304.3081</MSModSpec_averagemass>\n+ <MSModSpec_n15mass>0</MSModSpec_n15mass>\n+ <MSModSpec_residues>\n+ <MSModSpec_residues_E>Y</MSModSpec_residues_E>\n+ </MSModSpec_residues>\n+ <MSModSpec_unimod>731</MSModSpec_unimod>\n+ </MSModSpec>\n+ <MSModSpec>\n+ <MSModSpec_mod>\n+ <MSMod value="mod206">206</MSMod>\n+ </MSModSpec_mod>\n+ <MSModSpec_type>\n+ <MSModType value="modaa">0</MSModType>\n+ </MSModSpec_type>\n+ <MSModSpec_name>selenocysteine</MSModSpec_name>\n+ <MSModSpec_monomass>47.944449</MSModSpec_monomass>\n+ <MSModSpec_averagemass>46.8950</MSModSpec_averagemass>\n+ <MSModSpec_n15mass>0</MSModSpec_n15mass>\n+ <MSModSpec_residues>\n+ <MSModSpec_residues_E>C</MSModSpec_residues_E>\n+ </MSModSpec_residues>\n+ <MSModSpec_unimod>162</MSModSpec_unimod>\n+ </MSModSpec>\n+ <MSModSpec>\n+ <MSModSpec_mod>\n+ <MSMod value="mod207">207</MSMod>\n+ </MSModSpec_mod>\n+ <MSModSpec_type>\n+ <MSModType value="modaa">0</MSModType>\n+ </MSModSpec_type>\n+ <MSModSpec_name>carboxymethylated selenocysteine</MSModSpec_name>\n+ <MSModSpec_monomass>105.949928</MSModSpec_monomass>\n+ <MSModSpec_averagemass>104.9311</MSModSpec_averagemass>\n+ <MSModSpec_n15mass>0</MSModSpec_n15mass>\n+ <MSModSpec_residues>\n+ <MSModSpec_residues_E>C</MSModSpec_residues_E>\n+ </MSModSpec_residues>\n+ </MSModSpec>\n+</MSModSpecSet>\n' |
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| diff -r 000000000000 -r 0578e296cab4 searchGUI_usermods.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/searchGUI_usermods.xml Fri May 10 17:58:22 2013 -0400 |
| b |
| b'@@ -0,0 +1,455 @@\n+<?xml version="1.0"?>\n+<MSModSpecSet\n+xmlns="http://www.ncbi.nlm.nih.gov"\n+xmlns:xs="http://www.w3.org/2001/XMLSchema-instance"\n+xs:schemaLocation="http://www.ncbi.nlm.nih.gov OMSSA.xsd"\n+>\n+\n+\t<MSModSpec>\n+\t\t<MSModSpec_mod>\n+\t\t\t<MSMod value="usermod1">119</MSMod>\n+\t\t</MSModSpec_mod>\n+\t\t<MSModSpec_type>\n+\t\t\t<MSModType value="modnp">5</MSModType>\n+\t\t</MSModSpec_type>\n+\t\t<MSModSpec_name>dimethyl 2d n-terminus</MSModSpec_name>\n+\t\t<MSModSpec_monomass>32.0564</MSModSpec_monomass>\n+\t\t<MSModSpec_averagemass>0</MSModSpec_averagemass>\n+\t\t<MSModSpec_n15mass>0</MSModSpec_n15mass>\n+\t</MSModSpec>\n+\t<MSModSpec>\n+\t\t<MSModSpec_mod>\n+\t\t\t<MSMod value="usermod2">120</MSMod>\n+\t\t</MSModSpec_mod>\n+\t\t<MSModSpec_type>\n+\t\t\t<MSModType value="modaa">0</MSModType>\n+\t\t</MSModSpec_type>\n+\t\t<MSModSpec_name>dimethyl 2d k</MSModSpec_name>\n+\t\t<MSModSpec_monomass>32.0564</MSModSpec_monomass>\n+\t\t<MSModSpec_averagemass>0</MSModSpec_averagemass>\n+\t\t<MSModSpec_n15mass>0</MSModSpec_n15mass>\n+\t\t<MSModSpec_residues>\n+\t\t\t<MSModSpec_residues_E>K</MSModSpec_residues_E>\n+\t\t</MSModSpec_residues>\n+\t</MSModSpec>\n+\t<MSModSpec>\n+\t\t<MSModSpec_mod>\n+\t\t\t<MSMod value="usermod3">121</MSMod>\n+\t\t</MSModSpec_mod>\n+\t\t<MSModSpec_type>\n+\t\t\t<MSModType value="modaa">0</MSModType>\n+\t\t</MSModSpec_type>\n+\t\t<MSModSpec_name>gtp desthiobiotinc12</MSModSpec_name>\n+\t\t<MSModSpec_monomass>196.121178</MSModSpec_monomass>\n+\t\t<MSModSpec_averagemass>0</MSModSpec_averagemass>\n+\t\t<MSModSpec_n15mass>0</MSModSpec_n15mass>\n+\t\t<MSModSpec_residues>\n+\t\t\t<MSModSpec_residues_E>K</MSModSpec_residues_E>\n+\t\t</MSModSpec_residues>\n+\t</MSModSpec>\n+\t<MSModSpec>\n+\t\t<MSModSpec_mod>\n+\t\t\t<MSMod value="usermod4">122</MSMod>\n+\t\t</MSModSpec_mod>\n+\t\t<MSModSpec_type>\n+\t\t\t<MSModType value="modaa">0</MSModType>\n+\t\t</MSModSpec_type>\n+\t\t<MSModSpec_name>gtp desthiobiotinc13</MSModSpec_name>\n+\t\t<MSModSpec_monomass>202.141307</MSModSpec_monomass>\n+\t\t<MSModSpec_averagemass>0</MSModSpec_averagemass>\n+\t\t<MSModSpec_n15mass>0</MSModSpec_n15mass>\n+\t\t<MSModSpec_residues>\n+\t\t\t<MSModSpec_residues_E>K</MSModSpec_residues_E>\n+\t\t</MSModSpec_residues>\n+\t</MSModSpec>\n+\t<MSModSpec>\n+\t\t<MSModSpec_mod>\n+\t\t\t<MSMod value="usermod5">123</MSMod>\n+\t\t</MSModSpec_mod>\n+\t\t<MSModSpec_type>\n+\t\t\t<MSModType value="modaa">0</MSModType>\n+\t\t</MSModSpec_type>\n+\t\t<MSModSpec_name>User modification 5</MSModSpec_name>\n+\t\t<MSModSpec_monomass>0</MSModSpec_monomass>\n+\t\t<MSModSpec_averagemass>0</MSModSpec_averagemass>\n+\t\t<MSModSpec_n15mass>0</MSModSpec_n15mass>\n+\t\t<MSModSpec_residues>\n+\t\t\t<MSModSpec_residues_E>X</MSModSpec_residues_E>\n+\t\t</MSModSpec_residues>\n+\t</MSModSpec>\n+\t<MSModSpec>\n+\t\t<MSModSpec_mod>\n+\t\t\t<MSMod value="usermod6">124</MSMod>\n+\t\t</MSModSpec_mod>\n+\t\t<MSModSpec_type>\n+\t\t\t<MSModType value="modaa">0</MSModType>\n+\t\t</MSModSpec_type>\n+\t\t<MSModSpec_name>User modification 6</MSModSpec_name>\n+\t\t<MSModSpec_monomass>0</MSModSpec_monomass>\n+\t\t<MSModSpec_averagemass>0</MSModSpec_averagemass>\n+\t\t<MSModSpec_n15mass>0</MSModSpec_n15mass>\n+\t\t<MSModSpec_residues>\n+\t\t\t<MSModSpec_residues_E>X</MSModSpec_residues_E>\n+\t\t</MSModSpec_residues>\n+\t</MSModSpec>\n+\t<MSModSpec>\n+\t\t<MSModSpec_mod>\n+\t\t\t<MSMod value="usermod7">125</MSMod>\n+\t\t</MSModSpec_mod>\n+\t\t<MSModSpec_type>\n+\t\t\t<MSModType value="modaa">0</MSModType>\n+\t\t</MSModSpec_type>\n+\t\t<MSModSpec_name>User modification 7</MSModSpec_name>\n+\t\t<MSModSpec_monomass>0</MSModSpec_monomass>\n+\t\t<MSModSpec_averagemass>0</MSModSpec_averagemass>\n+\t\t<MSModSpec_n15mass>0</MSModSpec_n15mass>\n+\t\t<MSModSpec_residues>\n+\t\t\t<MSModSpec_residues_E>X</MSModSpec_residues_E>\n+\t\t</MSModSpec_residues>\n+\t</MSModSpec>\n+\t<MSModSpec>\n+\t\t<MSModSpec_mod>\n+\t\t\t<MSMod value="usermod8">126</MSMod>\n+\t\t</MSModSpec_mod>\n+\t\t<MSModSpec_type>\n+\t\t\t<MSModType value="modaa">0</MSModType>\n+\t\t</MSModSpec_type>\n+\t\t<MSModSpec_name>User modification 8</MSModSpec_name>\n+\t\t<MSModSpec_monomass>0</MSModSpec_monomass>\n+\t\t<MSModSpec_averagemass>0</MSModSpec_averagemass>\n+\t\t<MSModSpec_n15mass>0</MSModSpec_n15mass>\n+\t\t<MSModSpec_residues>\n+\t\t\t<MSModSpec_residues_E>X</M'..b's>\n+\t</MSModSpec>\n+\t<MSModSpec>\n+\t\t<MSModSpec_mod>\n+\t\t\t<MSMod value="usermod23">154</MSMod>\n+\t\t</MSModSpec_mod>\n+\t\t<MSModSpec_type>\n+\t\t\t<MSModType value="modaa">0</MSModType>\n+\t\t</MSModSpec_type>\n+\t\t<MSModSpec_name>User modification 23</MSModSpec_name>\n+\t\t<MSModSpec_monomass>0</MSModSpec_monomass>\n+\t\t<MSModSpec_averagemass>0</MSModSpec_averagemass>\n+\t\t<MSModSpec_n15mass>0</MSModSpec_n15mass>\n+\t\t<MSModSpec_residues>\n+\t\t\t<MSModSpec_residues_E>X</MSModSpec_residues_E>\n+\t\t</MSModSpec_residues>\n+\t</MSModSpec>\n+\t<MSModSpec>\n+\t\t<MSModSpec_mod>\n+\t\t\t<MSMod value="usermod24">155</MSMod>\n+\t\t</MSModSpec_mod>\n+\t\t<MSModSpec_type>\n+\t\t\t<MSModType value="modaa">0</MSModType>\n+\t\t</MSModSpec_type>\n+\t\t<MSModSpec_name>User modification 24</MSModSpec_name>\n+\t\t<MSModSpec_monomass>0</MSModSpec_monomass>\n+\t\t<MSModSpec_averagemass>0</MSModSpec_averagemass>\n+\t\t<MSModSpec_n15mass>0</MSModSpec_n15mass>\n+\t\t<MSModSpec_residues>\n+\t\t\t<MSModSpec_residues_E>X</MSModSpec_residues_E>\n+\t\t</MSModSpec_residues>\n+\t</MSModSpec>\n+\t<MSModSpec>\n+\t\t<MSModSpec_mod>\n+\t\t\t<MSMod value="usermod25">156</MSMod>\n+\t\t</MSModSpec_mod>\n+\t\t<MSModSpec_type>\n+\t\t\t<MSModType value="modaa">0</MSModType>\n+\t\t</MSModSpec_type>\n+\t\t<MSModSpec_name>User modification 25</MSModSpec_name>\n+\t\t<MSModSpec_monomass>0</MSModSpec_monomass>\n+\t\t<MSModSpec_averagemass>0</MSModSpec_averagemass>\n+\t\t<MSModSpec_n15mass>0</MSModSpec_n15mass>\n+\t\t<MSModSpec_residues>\n+\t\t\t<MSModSpec_residues_E>X</MSModSpec_residues_E>\n+\t\t</MSModSpec_residues>\n+\t</MSModSpec>\n+\t<MSModSpec>\n+\t\t<MSModSpec_mod>\n+\t\t\t<MSMod value="usermod26">157</MSMod>\n+\t\t</MSModSpec_mod>\n+\t\t<MSModSpec_type>\n+\t\t\t<MSModType value="modaa">0</MSModType>\n+\t\t</MSModSpec_type>\n+\t\t<MSModSpec_name>User modification 26</MSModSpec_name>\n+\t\t<MSModSpec_monomass>0</MSModSpec_monomass>\n+\t\t<MSModSpec_averagemass>0</MSModSpec_averagemass>\n+\t\t<MSModSpec_n15mass>0</MSModSpec_n15mass>\n+\t\t<MSModSpec_residues>\n+\t\t\t<MSModSpec_residues_E>X</MSModSpec_residues_E>\n+\t\t</MSModSpec_residues>\n+\t</MSModSpec>\n+\t<MSModSpec>\n+\t\t<MSModSpec_mod>\n+\t\t\t<MSMod value="usermod27">158</MSMod>\n+\t\t</MSModSpec_mod>\n+\t\t<MSModSpec_type>\n+\t\t\t<MSModType value="modaa">0</MSModType>\n+\t\t</MSModSpec_type>\n+\t\t<MSModSpec_name>User modification 27</MSModSpec_name>\n+\t\t<MSModSpec_monomass>0</MSModSpec_monomass>\n+\t\t<MSModSpec_averagemass>0</MSModSpec_averagemass>\n+\t\t<MSModSpec_n15mass>0</MSModSpec_n15mass>\n+\t\t<MSModSpec_residues>\n+\t\t\t<MSModSpec_residues_E>X</MSModSpec_residues_E>\n+\t\t</MSModSpec_residues>\n+\t</MSModSpec>\n+\t<MSModSpec>\n+\t\t<MSModSpec_mod>\n+\t\t\t<MSMod value="usermod28">159</MSMod>\n+\t\t</MSModSpec_mod>\n+\t\t<MSModSpec_type>\n+\t\t\t<MSModType value="modaa">0</MSModType>\n+\t\t</MSModSpec_type>\n+\t\t<MSModSpec_name>User modification 28</MSModSpec_name>\n+\t\t<MSModSpec_monomass>0</MSModSpec_monomass>\n+\t\t<MSModSpec_averagemass>0</MSModSpec_averagemass>\n+\t\t<MSModSpec_n15mass>0</MSModSpec_n15mass>\n+\t\t<MSModSpec_residues>\n+\t\t\t<MSModSpec_residues_E>X</MSModSpec_residues_E>\n+\t\t</MSModSpec_residues>\n+\t</MSModSpec>\n+\t<MSModSpec>\n+\t\t<MSModSpec_mod>\n+\t\t\t<MSMod value="usermod29">160</MSMod>\n+\t\t</MSModSpec_mod>\n+\t\t<MSModSpec_type>\n+\t\t\t<MSModType value="modaa">0</MSModType>\n+\t\t</MSModSpec_type>\n+\t\t<MSModSpec_name>User modification 29</MSModSpec_name>\n+\t\t<MSModSpec_monomass>0</MSModSpec_monomass>\n+\t\t<MSModSpec_averagemass>0</MSModSpec_averagemass>\n+\t\t<MSModSpec_n15mass>0</MSModSpec_n15mass>\n+\t\t<MSModSpec_residues>\n+\t\t\t<MSModSpec_residues_E>X</MSModSpec_residues_E>\n+\t\t</MSModSpec_residues>\n+\t</MSModSpec>\n+\t<MSModSpec>\n+\t\t<MSModSpec_mod>\n+\t\t\t<MSMod value="usermod30">161</MSMod>\n+\t\t</MSModSpec_mod>\n+\t\t<MSModSpec_type>\n+\t\t\t<MSModType value="modaa">0</MSModType>\n+\t\t</MSModSpec_type>\n+\t\t<MSModSpec_name>User modification 30</MSModSpec_name>\n+\t\t<MSModSpec_monomass>0</MSModSpec_monomass>\n+\t\t<MSModSpec_averagemass>0</MSModSpec_averagemass>\n+\t\t<MSModSpec_n15mass>0</MSModSpec_n15mass>\n+\t\t<MSModSpec_residues>\n+\t\t\t<MSModSpec_residues_E>X</MSModSpec_residues_E>\n+\t\t</MSModSpec_residues>\n+\t</MSModSpec>\n+</MSModSpecSet>\n\\ No newline at end of file\n' |
| b |
| diff -r 000000000000 -r 0578e296cab4 searchgui_mods.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/searchgui_mods.loc Fri May 10 17:58:22 2013 -0400 |
| b |
| @@ -0,0 +1,210 @@ +methylation of k +oxidation of m +carboxymethyl c +carbamidomethyl c +deamidation of n and q +propionamide c +phosphorylation of s +phosphorylation of t +phosphorylation of y +m cleavage from protein n-term +acetylation of protein n-term +methylation of protein n-term +tri-methylation of protein n-term +beta methythiolation of d +methylation of q +tri-methylation of k +methylation of d +methylation of e +methylation of peptide c-term +tri-deuteromethylation of d +tri-deuteromethylation of e +tri-deuteromethylation of peptide c-term +n-formyl met addition +2-amino-3-oxo-butanoic acid t +acetylation of k +amidation of peptide c-term +beta-methylthiolation of d (duplicate of 13) +carboxyamidomethylation of k +carboxyamidomethylation of h +carboxyamidomethylation of d +carboxyamidomethylation of e +carbamylation of k +carbamylation of n-term peptide +citrullination of r +oxidation of c to cysteic acid +di-iodination of y +di-methylation of k +di-methylation of r +di-methylation of peptide n-term +oxidation of f to dihydroxyphenylalanine +gammathiopropionylation of k +gammathiopropionylation of peptide n-term +farnesylation of c +formylation of k +formylation of peptide n-term +oxidation of w to formylkynurenin +fluorophenylalanine +beta-carboxylation of d +gamma-carboxylation of e +geranyl-geranyl +glucuronylation of protein n-term +glutathione disulfide +ubiquitinylation residue +guanidination of k +oxidation of h to n +oxidation of h to d +homoserine +homoserine lactone +oxidation of w to hydroxykynurenin +hydroxylation of d +hydroxylation of k +hydroxylation of n +hydroxylation of p +hydroxylation of f +hydroxylation of y +iodination of y +oxidation of w to kynurenin +lipoyl k +methyl ester of peptide c-term (duplicate of 18) +methyl ester of d +methyl ester of e (duplicate of 17) +methyl ester of s +methyl ester of y +methyl c +methyl h +methyl n +methylation of peptide n-term +methyl r +myristoleylation of g +myristoyl-4h of g +myristoylation of peptide n-term g +myristoylation of k +formylation of protein n-term +nem c +nipcam +oxidation of w to nitro +oxidation of y to nitro +o18 on peptide n-term +di-o18 on peptide n-term +oxidation of h +oxidation of w +phosphopantetheine s +palmitoylation of c +palmitoylation of k +palmitoylation of s +palmitoylation of t +phosphorylation of s with prompt loss +phosphorylation of t with prompt loss +phosphorylation with prompt loss on y +phosphorylation with neutral loss on c +phosphorylation with neutral loss on d +phosphorylation with neutral loss on h +propionyl light k +propionyl light on peptide n-term +propionyl heavy k +propionyl heavy peptide n-term +pyridyl k +pyridyl peptide n-term +pyro-cmc +pyro-glu from n-term e +pyro-glu from n-term q +oxidation of p to pyroglutamic acid +s-pyridylethylation of c +semet +sulfation of y +sulphone of m +tri-iodination of y +tri-methylation of r +n-acyl diglyceride cysteine +icat light +icat heavy +camthiopropanoyl k +phosphorylation with neutral loss on s +phosphorylation with neutral loss on t +phosphorylation of s with etd loss +phosphorylation of t with etd loss +heavy arginine-13c6 +heavy arginine-13c6-15n4 +heavy lysine-13c6 +pngasf in o18 water +beta elimination of s +beta elimination of t +oxidation of c to sulfinic acid +arginine to ornithine +dehydro of s and t +carboxykynurenin of w +sumoylation of k +itraq114 on nterm +itraq114 on k +itraq114 on y +itraq115 on nterm +itraq115 on k +itraq115 on y +itraq116 on nterm +itraq116 on k +itraq116 on y +itraq117 on nterm +itraq117 on k +itraq117 on y +mmts on c +heavy lysine - 2h4 +heavy lysine - 13c6 15n2 +asparagine hexnac +asparagine dhexhexnac +serine hexnac +threonine hexnac +palmitoleyl of s +palmitoleyl of c +palmitoleyl of t +chd2-di-methylation of k +chd2-di-methylation of peptide n-term +maleimide-peo2-biotin of c +phosphorylation of h +oxidation of c +oxidation of y (duplicate of 64) +uniblue a on k +deamidation of n +trideuteration of l (silac) +tmt duplex on k +tmt duplex on n-term peptide +tmt 6-plex on k +tmt 6-plex on n-term peptide +itraq8plex:13c(7)15n(1) on nterm +itraq8plex:13c(7)15n(1) on k +itraq8plex:13c(7)15n(1) on y +itraq8plex:13c(6)15n(2) on nterm +itraq8plex:13c(6)15n(2) on k +itraq8plex:13c(6)15n(2) on y +selenocysteine +carboxymethylated selenocysteine +dimethyl 2d n-terminus +dimethyl 2d k +gtp desthiobiotinc12 +gtp desthiobiotinc13 +user modification 5 +user modification 6 +user modification 7 +user modification 8 +user modification 9 +user modification 10 +user modification 11 +user modification 12 +user modification 13 +user modification 14 +user modification 15 +user modification 16 +user modification 17 +user modification 18 +user modification 19 +user modification 20 +user modification 21 +user modification 22 +user modification 23 +user modification 24 +user modification 25 +user modification 26 +user modification 27 +user modification 28 +user modification 29 +user modification 30 |
| b |
| diff -r 000000000000 -r 0578e296cab4 searchgui_mods.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/searchgui_mods.loc.sample Fri May 10 17:58:22 2013 -0400 |
| b |
| @@ -0,0 +1,210 @@ +methylation of k +oxidation of m +carboxymethyl c +carbamidomethyl c +deamidation of n and q +propionamide c +phosphorylation of s +phosphorylation of t +phosphorylation of y +m cleavage from protein n-term +acetylation of protein n-term +methylation of protein n-term +tri-methylation of protein n-term +beta methythiolation of d +methylation of q +tri-methylation of k +methylation of d +methylation of e +methylation of peptide c-term +tri-deuteromethylation of d +tri-deuteromethylation of e +tri-deuteromethylation of peptide c-term +n-formyl met addition +2-amino-3-oxo-butanoic acid t +acetylation of k +amidation of peptide c-term +beta-methylthiolation of d (duplicate of 13) +carboxyamidomethylation of k +carboxyamidomethylation of h +carboxyamidomethylation of d +carboxyamidomethylation of e +carbamylation of k +carbamylation of n-term peptide +citrullination of r +oxidation of c to cysteic acid +di-iodination of y +di-methylation of k +di-methylation of r +di-methylation of peptide n-term +oxidation of f to dihydroxyphenylalanine +gammathiopropionylation of k +gammathiopropionylation of peptide n-term +farnesylation of c +formylation of k +formylation of peptide n-term +oxidation of w to formylkynurenin +fluorophenylalanine +beta-carboxylation of d +gamma-carboxylation of e +geranyl-geranyl +glucuronylation of protein n-term +glutathione disulfide +ubiquitinylation residue +guanidination of k +oxidation of h to n +oxidation of h to d +homoserine +homoserine lactone +oxidation of w to hydroxykynurenin +hydroxylation of d +hydroxylation of k +hydroxylation of n +hydroxylation of p +hydroxylation of f +hydroxylation of y +iodination of y +oxidation of w to kynurenin +lipoyl k +methyl ester of peptide c-term (duplicate of 18) +methyl ester of d +methyl ester of e (duplicate of 17) +methyl ester of s +methyl ester of y +methyl c +methyl h +methyl n +methylation of peptide n-term +methyl r +myristoleylation of g +myristoyl-4h of g +myristoylation of peptide n-term g +myristoylation of k +formylation of protein n-term +nem c +nipcam +oxidation of w to nitro +oxidation of y to nitro +o18 on peptide n-term +di-o18 on peptide n-term +oxidation of h +oxidation of w +phosphopantetheine s +palmitoylation of c +palmitoylation of k +palmitoylation of s +palmitoylation of t +phosphorylation of s with prompt loss +phosphorylation of t with prompt loss +phosphorylation with prompt loss on y +phosphorylation with neutral loss on c +phosphorylation with neutral loss on d +phosphorylation with neutral loss on h +propionyl light k +propionyl light on peptide n-term +propionyl heavy k +propionyl heavy peptide n-term +pyridyl k +pyridyl peptide n-term +pyro-cmc +pyro-glu from n-term e +pyro-glu from n-term q +oxidation of p to pyroglutamic acid +s-pyridylethylation of c +semet +sulfation of y +sulphone of m +tri-iodination of y +tri-methylation of r +n-acyl diglyceride cysteine +icat light +icat heavy +camthiopropanoyl k +phosphorylation with neutral loss on s +phosphorylation with neutral loss on t +phosphorylation of s with etd loss +phosphorylation of t with etd loss +heavy arginine-13c6 +heavy arginine-13c6-15n4 +heavy lysine-13c6 +pngasf in o18 water +beta elimination of s +beta elimination of t +oxidation of c to sulfinic acid +arginine to ornithine +dehydro of s and t +carboxykynurenin of w +sumoylation of k +itraq114 on nterm +itraq114 on k +itraq114 on y +itraq115 on nterm +itraq115 on k +itraq115 on y +itraq116 on nterm +itraq116 on k +itraq116 on y +itraq117 on nterm +itraq117 on k +itraq117 on y +mmts on c +heavy lysine - 2h4 +heavy lysine - 13c6 15n2 +asparagine hexnac +asparagine dhexhexnac +serine hexnac +threonine hexnac +palmitoleyl of s +palmitoleyl of c +palmitoleyl of t +chd2-di-methylation of k +chd2-di-methylation of peptide n-term +maleimide-peo2-biotin of c +phosphorylation of h +oxidation of c +oxidation of y (duplicate of 64) +uniblue a on k +deamidation of n +trideuteration of l (silac) +tmt duplex on k +tmt duplex on n-term peptide +tmt 6-plex on k +tmt 6-plex on n-term peptide +itraq8plex:13c(7)15n(1) on nterm +itraq8plex:13c(7)15n(1) on k +itraq8plex:13c(7)15n(1) on y +itraq8plex:13c(6)15n(2) on nterm +itraq8plex:13c(6)15n(2) on k +itraq8plex:13c(6)15n(2) on y +selenocysteine +carboxymethylated selenocysteine +dimethyl 2d n-terminus +dimethyl 2d k +gtp desthiobiotinc12 +gtp desthiobiotinc13 +user modification 5 +user modification 6 +user modification 7 +user modification 8 +user modification 9 +user modification 10 +user modification 11 +user modification 12 +user modification 13 +user modification 14 +user modification 15 +user modification 16 +user modification 17 +user modification 18 +user modification 19 +user modification 20 +user modification 21 +user modification 22 +user modification 23 +user modification 24 +user modification 25 +user modification 26 +user modification 27 +user modification 28 +user modification 29 +user modification 30 |
| b |
| diff -r 000000000000 -r 0578e296cab4 update.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/update.sh Fri May 10 17:58:22 2013 -0400 |
| [ |
| @@ -0,0 +1,35 @@ +#!/bin/bash + +LICENSE_FILE=LICENSE +# Ensure repository contains license file. +if [ ! -e "$LICENSE_FILE" ]; +then + wget http://www.apache.org/licenses/LICENSE-2.0.txt -O "$LICENSE_FILE" +fi + +# Run repository specific update actions. +if [ -f update_repo.sh ]; +then + ./update_repo.sh +fi + +wget https://raw.github.com/gist/3749747/README_GALAXYP.md -O README_GALAXYP.md + +# Create repository README +if [ ! -e README_REPO.md ]; +then + echo "TODO: Document this tool repository." > README_REPO.md +fi +cat README_REPO.md README_GALAXYP.md > README.md + + +# If version file exists, update all tools to this version +VERSION_FILE=version +if [ -e "$VERSION_FILE" ]; +then + VERSION=`cat $VERSION_FILE` + + # Replace tool version in each tool XML file ` + find -iname "*xml" -exec sed -i'' -e '0,/version="\(.\+\)"/s/version="\(.\+\)"/version="'$VERSION'"/1g' {} \; + +fi |