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COPYING test-data/._tinyoutput.cps test-data/tinydb.fasta test-data/tinyoutput.cps test-data/tinyspectra.mgf |
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#env.sh# LICENSE README.md README_GALAXYP.md README_REPO.md build_mods_loc.py datatypes_conf.xml dbtoolkit-4.2/LICENSE-2.0.txt dbtoolkit-4.2/dbtoolkit-4.2.jar dbtoolkit-4.2/lib/jargs-1.0.jar dbtoolkit-4.2/lib/jargs-1.0.jar~ dbtoolkit-4.2/lib/log4j-1.2.12.jar dbtoolkit-4.2/lib/utilities-3.8.7.jar peptide_shaker.xml peptideshaker.py repository_dependencies.xml reverse.py reverse.xml searchGUI_mods.xml searchGUI_usermods.xml searchgui_mods.loc searchgui_mods.loc.sample tool_dependencies.xml update.sh |
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| diff -r 186fdc4b3310 -r 6cdbfdffb38e #env.sh# --- a/#env.sh# Mon Sep 16 17:32:18 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,3 +0,0 @@ - -export PATH=/path/to/2134123412341/tint_proteomics_scripts/:$PATH - |
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| diff -r 186fdc4b3310 -r 6cdbfdffb38e COPYING --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/COPYING Wed Jun 25 11:49:19 2014 -0400 |
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| @@ -0,0 +1,121 @@ +Creative Commons Legal Code + +CC0 1.0 Universal + + CREATIVE COMMONS CORPORATION IS NOT A LAW FIRM AND DOES NOT PROVIDE + LEGAL SERVICES. DISTRIBUTION OF THIS DOCUMENT DOES NOT CREATE AN + ATTORNEY-CLIENT RELATIONSHIP. CREATIVE COMMONS PROVIDES THIS + INFORMATION ON AN "AS-IS" BASIS. CREATIVE COMMONS MAKES NO WARRANTIES + REGARDING THE USE OF THIS DOCUMENT OR THE INFORMATION OR WORKS + PROVIDED HEREUNDER, AND DISCLAIMS LIABILITY FOR DAMAGES RESULTING FROM + THE USE OF THIS DOCUMENT OR THE INFORMATION OR WORKS PROVIDED + HEREUNDER. + +Statement of Purpose + +The laws of most jurisdictions throughout the world automatically confer +exclusive Copyright and Related Rights (defined below) upon the creator +and subsequent owner(s) (each and all, an "owner") of an original work of +authorship and/or a database (each, a "Work"). + +Certain owners wish to permanently relinquish those rights to a Work for +the purpose of contributing to a commons of creative, cultural and +scientific works ("Commons") that the public can reliably and without fear +of later claims of infringement build upon, modify, incorporate in other +works, reuse and redistribute as freely as possible in any form whatsoever +and for any purposes, including without limitation commercial purposes. +These owners may contribute to the Commons to promote the ideal of a free +culture and the further production of creative, cultural and scientific +works, or to gain reputation or greater distribution for their Work in +part through the use and efforts of others. + +For these and/or other purposes and motivations, and without any +expectation of additional consideration or compensation, the person +associating CC0 with a Work (the "Affirmer"), to the extent that he or she +is an owner of Copyright and Related Rights in the Work, voluntarily +elects to apply CC0 to the Work and publicly distribute the Work under its +terms, with knowledge of his or her Copyright and Related Rights in the +Work and the meaning and intended legal effect of CC0 on those rights. + +1. 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Should any part of the License for any +reason be judged legally invalid or ineffective under applicable law, such +partial invalidity or ineffectiveness shall not invalidate the remainder +of the License, and in such case Affirmer hereby affirms that he or she +will not (i) exercise any of his or her remaining Copyright and Related +Rights in the Work or (ii) assert any associated claims and causes of +action with respect to the Work, in either case contrary to Affirmer's +express Statement of Purpose. + +4. Limitations and Disclaimers. + + a. No trademark or patent rights held by Affirmer are waived, abandoned, + surrendered, licensed or otherwise affected by this document. + b. Affirmer offers the Work as-is and makes no representations or + warranties of any kind concerning the Work, express, implied, + statutory or otherwise, including without limitation warranties of + title, merchantability, fitness for a particular purpose, non + infringement, or the absence of latent or other defects, accuracy, or + the present or absence of errors, whether or not discoverable, all to + the greatest extent permissible under applicable law. + c. Affirmer disclaims responsibility for clearing rights of other persons + that may apply to the Work or any use thereof, including without + limitation any person's Copyright and Related Rights in the Work. + Further, Affirmer disclaims responsibility for obtaining any necessary + consents, permissions or other rights required for any use of the + Work. + d. Affirmer understands and acknowledges that Creative Commons is not a + party to this document and has no duty or obligation with respect to + this CC0 or use of the Work. |
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| diff -r 186fdc4b3310 -r 6cdbfdffb38e LICENSE --- a/LICENSE Mon Sep 16 17:32:18 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,11 +0,0 @@ ---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 186fdc4b3310 -r 6cdbfdffb38e README.md --- a/README.md Mon Sep 16 17:32:18 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,40 +0,0 @@ -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 186fdc4b3310 -r 6cdbfdffb38e README_GALAXYP.md --- a/README_GALAXYP.md Mon Sep 16 17:32:18 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,22 +0,0 @@ -# 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 186fdc4b3310 -r 6cdbfdffb38e README_REPO.md --- a/README_REPO.md Mon Sep 16 17:32:18 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,18 +0,0 @@ -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 186fdc4b3310 -r 6cdbfdffb38e build_mods_loc.py --- a/build_mods_loc.py Mon Sep 16 17:32:18 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,12 +0,0 @@ -#!/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 186fdc4b3310 -r 6cdbfdffb38e datatypes_conf.xml --- a/datatypes_conf.xml Mon Sep 16 17:32:18 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,9 +0,0 @@ -<?xml version="1.0"?> -<datatypes> - <datatype_files> - <datatype_file name="peptideshaker.py"/> - </datatype_files> - <registration> - <datatype extension="cps" type="galaxy.datatypes.peptideshaker:Cps" display_in_upload="true" /> - </registration> -</datatypes> |
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| diff -r 186fdc4b3310 -r 6cdbfdffb38e dbtoolkit-4.2/LICENSE-2.0.txt --- a/dbtoolkit-4.2/LICENSE-2.0.txt Mon Sep 16 17:32:18 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,202 +0,0 @@\n-\n- Apache License\n- Version 2.0, January 2004\n- http://www.apache.org/licenses/\n-\n- TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION\n-\n- 1. Definitions.\n-\n- "License" shall mean the terms and conditions for use, reproduction,\n- and distribution as defined by Sections 1 through 9 of this document.\n-\n- "Licensor" shall mean the copyright owner or entity authorized by\n- the copyright owner that is granting the License.\n-\n- "Legal Entity" shall mean the union of the acting entity and all\n- other entities that control, are controlled by, or are under common\n- control with that entity. 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| diff -r 186fdc4b3310 -r 6cdbfdffb38e dbtoolkit-4.2/dbtoolkit-4.2.jar |
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| diff -r 186fdc4b3310 -r 6cdbfdffb38e dbtoolkit-4.2/lib/jargs-1.0.jar --- a/dbtoolkit-4.2/lib/jargs-1.0.jar Mon Sep 16 17:32:18 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,48 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="SearchGUI" version="1.13.1"> - <install version="1.0"> - <actions> - <action type="download_by_url">http://searchgui.googlecode.com/files/SearchGUI-1.13.1_mac_and_linux.zip</action> - <action type="shell_command">tar -xf $DIR_NAME/*.tar</action> - <action type="shell_command">cd $DIR_NAME</action> - <action type="shell_command">chmod -R $DIR_NAME/*resources</action> - <action type="move_directory_files"> - <source_directory>.</source_directory> - <destination_directory>$INSTALL_DIR/</destination_directory> - </action> - <action type="shell_command">mkdir -p $BIN_DIR</action> - <action type="set_environment"> - <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable> - </action> - </actions> - </install> - <readme> - This package downloads and installs the SearchGUI scripts develped as part of the Peptideshaker tool. - (https://github.com/jmchilton/peptide-shaker). - - </readme> - </package> - - <package name="PeptideShaker" version="0.20.1"> - <install version="1.0"> - <actions> - <action type="download_by_url">http://peptide-shaker.googlecode.com/files/PeptideShaker-0.20.1.zip</action> - <action type="shell_command">chmod -R o+w resources</action> - <action type="move_directory_files"> - <source_directory>.</source_directory> - <destination_directory>$INSTALL_DIR/</destination_directory> - </action> - <action type="shell_command">mkdir -p $BIN_DIR</action> - <action type="set_environment"> - <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable> - </action> - </actions> - </install> - <readme> - This package downloads and installs the peptideshaker tool as a part of the peptideshaker framework. - (https://github.com/jmchilton/peptide-shaker). - - </readme> - </package> -</tool_dependency> |
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| diff -r 186fdc4b3310 -r 6cdbfdffb38e dbtoolkit-4.2/lib/jargs-1.0.jar~ |
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| diff -r 186fdc4b3310 -r 6cdbfdffb38e dbtoolkit-4.2/lib/log4j-1.2.12.jar |
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| diff -r 186fdc4b3310 -r 6cdbfdffb38e dbtoolkit-4.2/lib/utilities-3.8.7.jar |
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| diff -r 186fdc4b3310 -r 6cdbfdffb38e peptide_shaker.xml --- a/peptide_shaker.xml Mon Sep 16 17:32:18 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,228 +0,0 @@\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- #from datetime import datetime\n- #set $exp_str = "Galaxy Experiment %s" % datetime.now().strftime("%Y%m%d%H%M%s") \n- #set $samp_str = "Sample %s" % datetime.now().strftime("%Y%m%d%H%M%s")\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 $input_database;\n- PeptideShakerCLI \\\n- -experiment \'$exp_str\' \\\n- -sample \'$samp_str\' \\ \n- -replicate 1 \\\n- -spectrum_files \\$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" help="Select FASTA database from history. Typically, a target-decoy database is incorporated into the Scaffold engine for FDR analysis"/>\n- <param format="mgf" name="peak_lists" type="data" multiple="true" label="Input Peak Lists (mgf)" help="Select appropriate MGF dataset(s) from history" />\n- <param name="precursor_ion_tol_units" type="select" label="Precursor Ion Tolerance Units" help="Select based on instrument used, as different machines provide different quality of spectra. ppm is a standard for most precursor ions">\n- <option value="1">P'..b' (FDR) levels at the peptide, protein, and peptide-spectral match (PSM) levels, as well as False Loss Rate (FLR) for PSM\xe2\x80\x99s and A score options for post-translational modifications (PTM\xe2\x80\x99s). See this link_ for more details\n-\n- .. _link: http://peptide-shaker.googlecode.com/svn-history/r1267/wiki/tutorial/6_ptm_analysis.docx" />\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" help="Filter based on peptide lengths, precursor mass error, E value errors from X! Tandem and OMSSA, and include/exclude unknown PTM\xe2\x80\x99s"/>\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" version="0.20.1">peptide_shaker</requirement>\n- <requirement type="package" version="1.14.4">searchgui</requirement>\n- </requirements>\n- <help>\n-**What it does**\n-\n-Runs multiple search engines (X! Tandem and OMSSA) on any number of MGF peak lists using the SearchGUI application and combines the results.\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 Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-peptideshaker\n- </help>\n-</tool>\n' |
| b |
| diff -r 186fdc4b3310 -r 6cdbfdffb38e peptideshaker.py --- a/peptideshaker.py Mon Sep 16 17:32:18 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,8 +0,0 @@ -from galaxy.datatypes.binary import Binary - - -class Cps(Binary): - """Class describing a PeptideShaker CPS files""" - file_ext = "cps" - -Binary.register_unsniffable_binary_ext('cps') |
| b |
| diff -r 186fdc4b3310 -r 6cdbfdffb38e repository_dependencies.xml --- a/repository_dependencies.xml Mon Sep 16 17:32:18 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,6 +0,0 @@ -<?xml version="1.0"?> -<repositories description="Required proteomics dependencies."> - <repository toolshed="http://toolshed.g2.bx.psu.edu" name="proteomics_datatypes" owner="iracooke" changeset_revision="f74290b136fc" /> - <repository toolshed="http://toolshed.g2.bx.psu.edu" name="package_searchgui_1_14_4" owner="galaxyp" changeset_revision="67de51d52907" /> - <repository toolshed="http://toolshed.g2.bx.psu.edu" name="package_peptideshaker_0_20_1" owner="galaxyp" changeset_revision="cfd55b6c4fa2" /> -</repositories> |
| b |
| diff -r 186fdc4b3310 -r 6cdbfdffb38e reverse.py --- a/reverse.py Mon Sep 16 17:32:18 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,50 +0,0 @@ -from os.path import dirname, join, abspath -import sys -from optparse import OptionParser -from ConfigParser import SafeConfigParser -import subprocess - -DEBUG = False - - -def main(): - (options, args) = _parse_args() - format_args = (options.input, options.output) - _run_shell("cat '%s' > '%s'" % format_args) - _run_dbtoolkit("com.compomics.dbtoolkit.toolkit.ReverseFASTADB", "'%s' | head --lines -4 >> '%s'" % \ - format_args) - - -def _run_shell(command): - if DEBUG: - print "Running shell command %s" % command - _exec(command) - - -def _run_dbtoolkit(java_class, args): - command_prefix = "java -cp %s" % _dbtoolkit_jar_path() - _exec("%s %s %s" % (command_prefix, java_class, args)) - - -def _dbtoolkit_jar_path(): - py_path = __file__ - jar_path = join(dirname(py_path), "dbtoolkit-4.2", "dbtoolkit-4.2.jar") - return jar_path - -def _exec(command): - proc = subprocess.Popen(args=command, shell=True) - return_code = proc.wait() - if return_code != 0: - print "Error executing command [%s], return code is %d" % (command, return_code) - sys.exit(return_code) - - -def _parse_args(): - parser = OptionParser() - parser.add_option("-i", "--input") - parser.add_option("-o", "--output") - return parser.parse_args() - - -if __name__ == "__main__": - main() |
| b |
| diff -r 186fdc4b3310 -r 6cdbfdffb38e reverse.xml --- a/reverse.xml Mon Sep 16 17:32:18 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,32 +0,0 @@ -<tool id="compomics_reverse" name="Create Target-Decoy Database" version="0.1.0"> - <description>Creates a target-decoy database for use with Peptide Shaker</description> - - <requirements> - </requirements> - - <command interpreter="python">reverse.py --input='$input' --output='$output'</command> - - <inputs> - <param format="fasta" name="input" type="data" label="FASTA Input" /> - </inputs> - - <outputs> - <data format="fasta" name="output" /> - </outputs> - - <help> -**What it does** - -Given an input database, this tool will produce a target-decoy -database in the format required by PeptideShaker using dbtoolkit. - ------- - -**Citation** - -For the underlying tool, please cite `Martens et al. DBToolkit: processing protein databases for peptide-centric proteomics. Bioinformatics (2005) vol. 21 (17) pp. 3584-5`. - -If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-peptideshaker . - - </help> -</tool> |
| b |
| diff -r 186fdc4b3310 -r 6cdbfdffb38e searchGUI_mods.xml --- a/searchGUI_mods.xml Mon Sep 16 17:32:18 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,3021 +0,0 @@\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' |
| b |
| diff -r 186fdc4b3310 -r 6cdbfdffb38e searchGUI_usermods.xml --- a/searchGUI_usermods.xml Mon Sep 16 17:32:18 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,455 +0,0 @@\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 186fdc4b3310 -r 6cdbfdffb38e searchgui_mods.loc --- a/searchgui_mods.loc Mon Sep 16 17:32:18 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,210 +0,0 @@ -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 186fdc4b3310 -r 6cdbfdffb38e searchgui_mods.loc.sample --- a/searchgui_mods.loc.sample Mon Sep 16 17:32:18 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,210 +0,0 @@ -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 186fdc4b3310 -r 6cdbfdffb38e test-data/._tinyoutput.cps |
| b |
| Binary file test-data/._tinyoutput.cps has changed |
| b |
| diff -r 186fdc4b3310 -r 6cdbfdffb38e test-data/tinydb.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tinydb.fasta Wed Jun 25 11:49:19 2014 -0400 |
| b |
| @@ -0,0 +1,24 @@ +>cds.comp107265_c0_seq1|m.36816 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.94 EValue:9.0e-68 +LKSSFESSFSIKSRDVTFGNSMNITMVPPELEFFKDNRHKEKSEMQDLNTRLESYLSVGKDDSDANLKLMQELEEIKNGIKTETNNIKATFEAELGQLKNLLDDIDHDKNQVIVIGDNNDEMYKDLEQRIKNYNDMEMIHLSKIRQLDNLLSNYGLKMNQLQKKIGFLCEEKDRDIESINKLRADIDVAKNDLSNEILLRTDAQNRCQSLEEDIEFTKEVHQRELSNMIALADYDPVSQSMDWWNDEFARCIKEIQDEYEDRLNNIQYDMDSHYNSKIQDVETTILQSSAKSEMLDQCSMLENSNAEIEDQTSELEKKNAMLKEQNDLLNRGIREIQSQFETLITEKQSEMLEIRKHFEQSLADLQAIVDDNLSLQMEIMSYKKLLECEELRVGIYPESNANENQGDQGQRQNEQITEPITETIPKRKKPERKISYQRSSKGPLTISECKSDGSYILIENMDQYDGQNLGGWRLVQNVDGMEEYDYTFSRYYLGPGESVKIWAENAGPKGVNDLVWDDLKCLGIGEKVITSLMNQKGKEKSSYTQKAIYKV +>cds.comp307584_c0_seq2|m.40556 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 39.47 EValue:1.0e-14 +DDNYDSLQYSFPKSDHQRKTTYQRSAKGPITITRVQPDGSYIEIENTNIAVNEDISGWKMVQCTDDKIYEYIFDDHVLNGGTCVKIWANGLSGKEENDLVWIDRTCLTTGSVVTTTLMDYNGNEKATFTQ +>cds.comp376950_c0_seq1|m.42080 RecName: Full=60 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 41.38 EValue:1.0e-32 +KELEDINEDNLGRLRRQDEDVSNYEAQNASLRRKCDNLQADKDRDRNNVEKLKGEVTSLRNDLMMETVSRIDSQNKCQTLREELEFLKDIHSQELKELSPTLGKDPFAKSKEWWSSEFSNCIREIQEEYDNRLDSIKTDMDNYYTLKVQEIQTGAAR +>cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67 +METTKERKEKSTVVTKRQSMGATAHVQPKFIQVNRRSHVVGAGLGGGSMGSMNQSMSLHGGRASLGMAAGVAGGIATKDMGTMKVKREGEKKDMQNLNDRFAGYIAKVRSLQAENEQLRLKLSKKRREFDVEPLKEAYQAEIDEAKNLLLDANKENGELKISITTYEEEIEDLHATARINEDRIDELQDKVNKLIDENSHREAECSMLHKKLDELEKQVAHWRAKYNEVNTQLQATRADLKDETQQRIFLQQKVGNLEEELEFLRSVTDAEIKEYKAMLSKEDDTGTNVSAAWNNEMSNCMKELREEYDQRLADISDEMSARYESQLSQIRQSAHAEPVAAVHTKSEKSTGMVSVQKDMRIKELESQLERMKMEIITITNQLQRSNEDLENEKDLRTTEVNKLHVEMESMIEELQMLMDAKLSLELEIAAYRKLLEGEENRISTGYITENIGGFRSEAGDNLANILEFGSGGGGGGGGGGSGSGSGSGLAGDSASTSTLTGRLTIQRSSKSVISIGEVESEGQYVTLENTSSGRSKTSVNMKGWKLDRLISATSISPEHKIDFLFKDPVVLEGEQSIKIWAKNYQKMAKKGDIIATVDEWGPVNRNSVFSLYDEKDALKANLSTKVVT +>cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 +METTKERKEKSTVVTKRQSMGATAHVQPKFIQVNRRSHVVGAGLGGGSMGSMNQSMSLHGGRASLGMAAGVAGGIATKDMGTMKVKREGEKKDMQNLNDRFAGYIAKVRSLQAENEQLRLKLSKKRREFDVEPLKEAYQAEIDEAKNLLLDANKENGELKISITTYEEEIEDLHATARINEDRIDELQDKVNKLIDENSHREAECSMLHKKLDELEKQVAHWRAKYNEVNTQLQATRADLKDETQQRIFLQQKVGNLEEELEFLRSVTDAEIKEYKAMLSKEDDTGTNVSAAWNNEMSNCMKELREEYDQRLADISDEMSARYESQLSQIRQSAHAEPVAAVHTKSEKSTGMVSVQKDMRIKELESQLERMKMEIITITNQLQRSNEDLENEKDLRTTEVNKLHVEMESMIEELQMLMDAKLSLELEIAAYRKLLEGEENRISTGYITENIGGFRSEAGDNLANILEFGSGGGGGGGGGGSGSGSGSGLAGDSGRLTIQRSSKSVISIGEVESEGQYVTLENTSSGRSKTSVNMKGWKLDRLISATSISPEHKIDFLFKDPVVLEGEQSIKIWAKNYQKMAKKGDIIATVDEWGPVNRNSVFSLYDEKDALKANLSTKVVT +>cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10 +SGLAGDSDTMRASTSTLTGRLTIQRSSKSVISIGEVESEGQYVTLENTSSGRSKTSVNMKGWKLDRLISATSISPEHKIDFLFKDPVVLEGEQSIKIWAKNYQKMAKKGDIIATVDEWGPVNRNSVFSLYDEKDALKANLSTKVVT +>cds.comp41890_c0_seq1|m.9546 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 38.58 EValue:4.0e-20 +YQSPTPALVKGELQEHSTYRKNNKGPVAISETDRDGSFILLENTSNSHTVDLSGWKIMQNSDNIDISEYEIENLVLKPGGFAKVWANGMGDPNSGDLVWHNKSRLGVGAKVNTVLLNTRGDEKATYNLETTYNL +>cds.comp52727_c0_seq1|m.18670 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 34.52 EValue:1.0e-91 +MEKQGVETRQTVTTSRQSVNYKPFTQSKNIVINRVSLSPGTAMSTMQRSRSSMSSGLGLGGHLQAGVLGNISHKGVASMKLKREGEKKELQDLNERLANFIEQARFLEAENKALRDALNKSKKDFDPEPLKQMYQIEINEAKKLLDDANNDNGNLKVRINTLEDELEDLRAQLRHSNDVNDQLQNNIDTLNDDIARRIADNEMLKRKVQELEKQLADWKAKYAHVDTQLQGLRIDLQEETCQRLAESTRAQALEEELNFLRSVTDAEIKEYKAMLMKEDNVPQMREYWNNELSKCMREIRDEYDNQLNLLSADLESKYQVQLNEIRLGATKGNAESAQASEENRRLRSQITDKDSHMMDLQSQIDKLKSQVHLLTSELDSTTAELDNEKTLRVSEVQKLNTELEGVIKELQLLMDAKLSLELEIAAYRKLLEVEENRLSIGSMTQMVGGYRGQTEDALANILERSGASFEASSSMGESGTTSITTGRVTMQRSSKGVISIAEVDNTGRYVTLDNTSTTRMKRLQNLKGWKIKREFIRTNSLQELSFEYIINRDTSLDAQQNIRVWAKNFEKDPEIKPDDIISSVADWGQVNRNSIITLYDENGVEKATLTIKVVF +>cds.comp52727_c0_seq2|m.18672 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 35.0 EValue:3.0e-92 +MEKQGVETRQTVTTSRQSVNYKPFTQSKNIVINRVSLSPGTAMSTMQRSRSSMSSGLGLGGHLQAGVLGNISHKGVASMKLKREGEKKELQDLNERLANFIEQARFLEAENKALRDALNKSKKDFDPEPLKQMYQIEINEAKKLLDDANNDNGNLKVRINTLEDELEDLRAQLRHSNDVNDQLQNNIDTLNDDIARRIADNEMLKRKVQELEKQLADWKAKYAHVDTQLQGLRIDLQEETCQRLAESTRAQALEEELNFLRSVTDAEIKEYKAMLMKEDNVPQMREYWNNELSKCMREIRDEYDNQLNLLSADLESKYQVQLNEIRLGATKGNAESAQASEENRRLRSQITDKDSHMMDLQSQIDKLKSQVHLLTSELDSTTAELDNEKTLRVSEVQKLNTELEGVIKELQLLMDAKLSLELEIAAYRKLLEVEENRLSIGSMTQMVGGYRGQTEDALANILERSGASFEASSSMGESGRVTMQRSSKGVISIAEVDNTGRYVTLDNTSTTRMKRLQNLKGWKIKREFIRTNSLQELSFEYIINRDTSLDAQQNIRVWAKNFEKDPEIKPDDIISSVADWGQVNRNSIITLYDENGVEKATLTIKVVF +>cds.comp55448_c0_seq1|m.24261 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 96.04 EValue:0.0 +MRRIKKKITLDVRVTELIDQLERQQKELEESRTYHQIDQEQIARQNQQLADLEGEISMLRRSIESLEKEKMRQSNILAKMNDELEKLRMDLNNETINHLDAENRRQTLEEELEFQKDVHAQELKELAALAYRDTTAENREFWRNELAQAIRDIQQEYDAKCDQMRGDIEAYYNLKVQEFRTGATKQNMEVTRNKEENTKLRSNMNEVRNRLADLEARNAQLERTNQDLLRDLEEKDRQNELESCQYKEEITKLRGEMESILKELQDLMDIKLSLELEIAAYRKLLEGEESRVGMKQIVEQVVGARPNEAEVLSSILTRSEGGYEATGDSQISMKMMRGELAAKTTYQRTSKGPVSIKEADSQGQFIALETKKEENITGWKIVRKVDDNMVYSYEIPNVVLKTGTVIKIWSKSHQAQARGDDIVSRENDTWGTGSNVVTILQNEKGEEKANYTQNTVYQ +>cds.comp55448_c0_seq1|m.24262 RecName: Full=60 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 91.49 EValue:5.0e-87 +MSGGFSYSAKIHPRTGYVSRTSQSPYRSSMGSNAAFTRSYEFNYGATAMPGAYANISSTGVNHVKANREREKQDMRDLNERFANYIEKVRFLEAQNKKLAGELEELKSKWGKETSAIKEMYETELEEARKLIDATNKEKNYLGRESN +>cds.comp8310_c0_seq2|m.1138 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 22.01 EValue:2.0e-16 +FKDTCIRDKTDMKGLNERLSEFIEVARYNAILAKKLEKTIKRFHSQEIPEDVERIYEATIKKLRKLLVVFENERDNERAKNLKLQTECAKLKESLEDLKAKEIENRDRLISKFKILEDLQSKAIRIEKNIEIVAEENVLKNNKIEKLKKHFENLKSKITSERRNRSTHKESYDEVKEDFGIFKELKNQQLSSVRFPKYKDSIKYLRKQWSNEFSKCIKELQNEYESRVSSVKEELESNYCTKTEEIQNYVLKSNYESDFLKNRNLVAEESMNMLKNKFKEAKKENVLLNHEKEELEIEFNKSKNEYDHLAEEKNNEILNFKEYAEKILIQLTEILEINNHLQFEIEYYKTVITSGETKIDFDFDGLDDECMTSINSELP |
| b |
| diff -r 186fdc4b3310 -r 6cdbfdffb38e test-data/tinyoutput.cps |
| b |
| Binary file test-data/tinyoutput.cps has changed |
| b |
| diff -r 186fdc4b3310 -r 6cdbfdffb38e test-data/tinyspectra.mgf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tinyspectra.mgf Wed Jun 25 11:49:19 2014 -0400 |
| b |
| b'@@ -0,0 +1,6153 @@\n+BEGIN IONS\r\n+TITLE= Cmpd 636, +MSn(730.3981), 66.9 min\r\n+PEPMASS=730.39814\t92569\r\n+CHARGE=2+\r\n+156.06738\t122\t\r\n+175.10440\t1049\t\r\n+186.08322\t120\t\r\n+187.12501\t241\t\r\n+188.06515\t494\t1+\r\n+193.09503\t180\t\r\n+197.12522\t208\t\r\n+199.17309\t1374\t1+\r\n+204.08687\t454\t1+\r\n+213.14347\t128\t\r\n+215.11998\t747\t1+\r\n+227.17167\t1524\t1+\r\n+229.12416\t156\t\r\n+233.09327\t3574\t1+\r\n+236.99586\t113\t\r\n+243.14264\t571\t1+\r\n+244.07481\t236\t\r\n+245.12901\t240\t\r\n+246.12647\t275\t\r\n+256.20038\t432\t1+\r\n+258.12496\t133\t\r\n+260.19976\t423\t\r\n+261.09190\t17853\t1+\r\n+270.16206\t114\t\r\n+274.12614\t207\t\r\n+283.15366\t136\t\r\n+284.18559\t406\t1+\r\n+286.14626\t237\t\r\n+287.10013\t105\t\r\n+301.15759\t131\t\r\n+303.17924\t2962\t1+\r\n+310.21264\t944\t1+\r\n+315.13250\t122\t\r\n+316.16696\t108\t\r\n+326.16601\t145\t\r\n+328.21268\t874\t1+\r\n+335.13393\t406\t1+\r\n+338.20704\t186\t\r\n+339.16449\t110\t\r\n+342.17857\t106\t\r\n+344.13585\t148\t\r\n+346.17426\t809\t1+\r\n+356.21762\t685\t1+\r\n+358.15839\t265\t\r\n+359.26213\t106\t\r\n+362.14671\t528\t1+\r\n+366.16564\t103\t\r\n+370.14930\t136\t\r\n+374.17893\t18824\t1+\r\n+380.20460\t141\t\r\n+384.22488\t193\t\r\n+387.21562\t161\t\r\n+388.26191\t188\t\r\n+411.26204\t166\t\r\n+415.22868\t119\t\r\n+416.26432\t2092\t1+\r\n+421.21633\t119\t\r\n+423.29102\t378\t1+\r\n+425.19591\t120\t\r\n+429.24479\t213\t\r\n+430.23711\t292\t\r\n+431.20421\t187\t\r\n+436.18404\t103\t\r\n+436.75217\t164\t\r\n+437.24576\t210\t\r\n+439.24189\t686\t1+\r\n+441.27348\t282\t\r\n+442.22757\t266\t\r\n+443.24151\t187\t\r\n+447.25851\t136\t\r\n+448.23776\t110\t\r\n+451.24187\t133\t\r\n+454.21183\t186\t\r\n+455.28038\t426\t1+\r\n+457.22899\t1666\t1+\r\n+459.26367\t3533\t1+\r\n+470.24566\t153\t\r\n+471.25916\t214\t\r\n+472.22369\t149\t\r\n+475.22776\t2402\t1+\r\n+476.74146\t108\t\r\n+478.76406\t148\t\r\n+479.26444\t182\t\r\n+481.79718\t109\t\r\n+482.23965\t265\t\r\n+484.28349\t122\t\r\n+485.26864\t194\t\r\n+487.26385\t8530\t1+\r\n+487.76699\t2322\t2+\r\n+492.79121\t214\t\r\n+493.27987\t223\t\r\n+496.25943\t155\t\r\n+498.26458\t113\t\r\n+499.26123\t188\t\r\n+500.25926\t116\t\r\n+502.31880\t144\t\r\n+503.29803\t113\t\r\n+505.25694\t134\t\r\n+507.23129\t148\t\r\n+509.26114\t112\t\r\n+512.29082\t270\t\r\n+516.25599\t158\t\r\n+517.20915\t133\t\r\n+517.28047\t196\t\r\n+518.26358\t209\t\r\n+519.25298\t141\t\r\n+524.32901\t134\t\r\n+525.28341\t246\t\r\n+525.73648\t129\t\r\n+526.28178\t183\t\r\n+527.27825\t442\t1+\r\n+530.27675\t144\t\r\n+531.28549\t121\t\r\n+533.28116\t104\t\r\n+534.11078\t105\t\r\n+534.80853\t658\t2+\r\n+536.27223\t192\t\r\n+537.26164\t134\t\r\n+538.59905\t107\t\r\n+539.27286\t106\t\r\n+540.27423\t189\t\r\n+541.25963\t119\t\r\n+542.30271\t822\t1+\r\n+543.81900\t3982\t2+\r\n+544.31230\t3061\t1+\r\n+546.73644\t112\t\r\n+550.76990\t117\t\r\n+551.22357\t107\t\r\n+552.32208\t662\t1+\r\n+555.31596\t235\t\r\n+556.27474\t176\t\r\n+558.29453\t154\t\r\n+559.29947\t142\t\r\n+560.30729\t1143\t1+\r\n+567.24429\t116\t\r\n+569.25892\t228\t\r\n+570.29732\t7469\t1+\r\n+575.31645\t290\t\r\n+580.32039\t169\t\r\n+584.32568\t221\t\r\n+585.29844\t155\t\r\n+588.30437\t6069\t1+\r\n+591.34398\t1900\t2+\r\n+593.19489\t103\t\r\n+594.32473\t103\t\r\n+598.30327\t171\t\r\n+600.36464\t3642\t2+\r\n+602.30487\t970\t1+\r\n+608.28169\t160\t\r\n+609.27493\t133\t\r\n+614.83731\t112\t\r\n+615.27771\t193\t\r\n+617.30438\t138\t\r\n+618.32896\t149\t\r\n+619.33485\t160\t\r\n+620.31542\t115\t\r\n+620.81406\t230\t\r\n+622.32210\t208\t\r\n+623.32017\t135\t\r\n+624.28638\t129\t\r\n+626.34792\t207\t\r\n+628.34041\t189\t\r\n+629.25299\t114\t\r\n+630.37407\t171\t\r\n+632.31114\t124\t\r\n+634.29651\t120\t\r\n+636.28359\t105\t\r\n+637.35608\t222\t\r\n+638.34750\t245\t\r\n+639.34410\t173\t\r\n+641.33612\t839\t1+\r\n+646.33654\t117\t\r\n+647.19559\t1433\t1+\r\n+649.19722\t1100\t1+\r\n+651.31229\t136\t\r\n+653.31813\t227\t\r\n+654.33373\t187\t\r\n+655.38010\t176\t\r\n+656.35127\t649\t1+\r\n+658.36493\t6652\t1+\r\n+664.87410\t264\t\r\n+665.36702\t578\t1+\r\n+668.36277\t108\t\r\n+669.88900\t118\t\r\n+671.36838\t605\t1+\r\n+673.38354\t533\t1+\r\n+674.31604\t138\t\r\n+680.33315\t119\t\r\n+682.86635\t152\t\r\n+683.37863\t4557\t1+\r\n+689.35741\t806\t1+\r\n+693.34598\t140\t\r\n+695.38537\t116\t\r\n+696.37550\t112\t\r\n+697.39934\t146\t\r\n+698.39359\t132\t\r\n+699.36352\t115\t\r\n+701.38282\t1437\t1+\r\n+706.39934\t164\t\r\n+707.37693\t151\t\r\n+707.86433\t178\t\r\n+710.37380\t213\t\r\n+712.37982\t250\t\r\n+712.89070\t251\t\r\n+713.37280\t260\t\r\n+713.88658\t123\t\r\n+715.37058\t153\t\r\n+716.18442\t4201\t1+\r\n+716.77672\t108\t\r\n+718.18321\t2451\t1+\r\n+718.88287\t2231\t2+\r\n+720.98962\t121\t\r\n+721.39031\t3707\t2+\r\n+724.88574\t175\t\r\n+725.39311\t174\t\r\n+725.86419\t119\t\r\n+726.38179\t168\t\r\n+726.88029\t279\t\r\n+727.39635\t1151\t2+\r\n+729.38218\t580\t\r\n+72'..b'\t344\t\r\n+361.68768\t266\t2+\r\n+367.19099\t244\t\r\n+368.24304\t252\t\r\n+378.20951\t295\t\r\n+379.04198\t240\t\r\n+380.15312\t263\t\r\n+386.22588\t261\t\r\n+394.20036\t279\t\r\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IONS\r\n+\r\n' |
| b |
| diff -r 186fdc4b3310 -r 6cdbfdffb38e tool_dependencies.xml --- a/tool_dependencies.xml Mon Sep 16 17:32:18 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,9 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="searchgui" version="1.14.1"> - <repository toolshed="http://toolshed.g2.bx.psu.edu" name="package_searchgui_1_14_4" owner="galaxyp" changeset_revision="67de51d52907" /> - </package> - <package name="peptide_shaker" version="0.20.1"> - <repository toolshed="http://toolshed.g2.bx.psu.edu" name="package_peptideshaker_0_20_1" owner="galaxyp" changeset_revision="cfd55b6c4fa2" /> - </package> -</tool_dependency> |
| b |
| diff -r 186fdc4b3310 -r 6cdbfdffb38e update.sh --- a/update.sh Mon Sep 16 17:32:18 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,35 +0,0 @@ -#!/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 |