Mercurial > repos > bgruening > upload_testing
changeset 105:f258fbfead4b draft
Uploaded
| author | bgruening |
|---|---|
| date | Fri, 11 Apr 2014 16:32:28 -0400 |
| parents | 0b732f3cfad0 |
| children | cd64faa6b531 |
| files | COPYING README.md 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/log4j-1.2.12.jar dbtoolkit-4.2/lib/utilities-3.8.7.jar osra.py osra.xml peptide_shaker.xml readme repository_dependencies.xml reverse.py reverse.xml searchgui_mods.loc.sample test_data/2008001635_153_chem.png test_data/2008001635_153_chem.smi test_data/CID_2244.png test_data/CID_2244.sdf tool_dependencies.xml |
| diffstat | 21 files changed, 990 insertions(+), 348 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/COPYING Fri Apr 11 16:32:28 2014 -0400 @@ -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. 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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. 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.md Fri Apr 11 16:32:28 2014 -0400 @@ -0,0 +1,63 @@ +GalaxyP - PeptideShaker +======================= + +* Home: <https://bitbucket.org/galaxyp/peptideshaker> +* Galaxy Tool Shed: <http://toolshed.g2.bx.psu.edu/view/galaxyp/peptideshaker> +* Tool ID: `peptideshaker` +* Tool Type: `default` + + +Description +----------- + +Peform protein identification combining X! Tandem and OMSSA (using SearchGUI) and PeptideShaker pipeline. + +Tool wrapper for SearchGUI and 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. + +Note: + +- SearchGUI requires a version greater than 1.12.2 which contained several bugs preventing this from working on the command-line and via Linux. + +- PeptideShaker may require xvfb to simulate an X environment if this is installed on a headless server. + +See: + +* <https://code.google.com/p/peptide-shaker/> +* <https://code.google.com/p/searchgui/> + + +GalaxyP Community +----------------- + +Current governing community policies for [GalaxyP](https://bitbucket.org/galaxyp/) and other information can be found at: + +<https://bitbucket.org/galaxyp/galaxyp> + + +License +------- + +Copyright (c) 2014 Regents of the University of Minnesota and Authors listed below. + +To the extent possible under law, the author(s) have dedicated all copyright and related and neighboring rights to this software to the public domain worldwide. This software is distributed without any warranty. + +You should have received a copy of the CC0 Public Domain Dedication along with this software. If not, see <https://creativecommons.org/publicdomain/zero/1.0/>. + +You can copy, modify, distribute and perform the work, even for commercial purposes, all without asking permission. + + +Contributing +------------ + +Contributions to this repository are reviewed through pull requests. If you would like your work acknowledged, please also add yourself to the Authors section. If your pull request is accepted, you will also be acknowledged in <https://bitbucket.org/galaxyp/galaxyp/CONTRIBUTORS.md> unless you opt-out. + + +Authors +------- + +Authors and contributors: + +* Cody Wang +* Fred Sadler +* John Chilton <jmchilton@gmail.com> +* Minnesota Supercomputing Institute, Univeristy of Minnesota
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/datatypes_conf.xml Fri Apr 11 16:32:28 2014 -0400 @@ -0,0 +1,6 @@ +<?xml version="1.0"?> +<datatypes> + <registration> + <datatype extension="cps" type="galaxy.datatypes.binary:Binary" subclass="True" display_in_upload="true" /> + </registration> +</datatypes>
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/dbtoolkit-4.2/lib/jargs-1.0.jar Fri Apr 11 16:32:28 2014 -0400 @@ -0,0 +1,48 @@ +<?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>
--- a/osra.py Thu Apr 03 06:07:32 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,27 +0,0 @@ -#!usr/bin/env python - -import os, sys -import subprocess - -""" - OSRA_DATA_FILES is set during the toolshed Installation - If it is not set, use the standard configuration of OSRA. - That means we need to delete argument 4-7. - That script is a hack, because we do not know the content of OSRA_DATA_FILES at xml evaluation time. - - osra -f $oformat $infile - -l \$OSRA_DATA_FILES/spelling.txt -a \$OSRA_DATA_FILES/superatom.txt - > $outfile -""" - -if not os.path.exists(sys.argv[7]): - # OSRA_DATA_FILES path is not set or the spelling file is not existent - sys.argv.pop(7) # superatom.txt path - sys.argv.pop(6) # -a - sys.argv.pop(5) # speling.txt path - sys.argv.pop(4) # -l - -sys.argv[0] = 'osra' -subprocess.call(sys.argv, stdout=sys.stdout) - -
--- a/osra.xml Thu Apr 03 06:07:32 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,74 +0,0 @@ -<tool id="ctb_osra" name="Molecule recognition" version="0.3"> - <description>in Images or PDF documents (OSRA)</description> - <requirements> - <requirement type="package" version="2.0.0">osra</requirement> - <requirement type="package" version="2.3.2">openbabel</requirement> - <requirement type="package" version="1.3.18">graphicsmagick</requirement> - </requirements> - <command interpreter='python'> - ## OSRA_DATA_FILES is set during the toolshed Installation - ## if it is not set, use the standard configuration and hope the best - osra.py -f $oformat $infile - -l \$OSRA_DATA_FILES/spelling.txt -a \$OSRA_DATA_FILES/superatom.txt - - ## further additions of OSRA parameter should go after -l and -a - ## because -l and -a can be removed by the python wrapper - - $confidence - $adaptive - $thinning - - > $outfile - </command> - <inputs> - <param name="infile" type="data" format="png,pdf" label="Image or PDF with molecules"/> - <param name="oformat" type="select" label="Output molecule format"> - <option value="can">SMILES</option> - <option value="sdf">SDF</option> - </param> - <param name="confidence" type="boolean" label="Print out confidence estimate (-p)" truevalue="-p" falsevalue="" checked="true" /> - <param name="adaptive" type="boolean" label="Adaptive thresholding pre-processing, useful for low light/low contrast images (-i)" truevalue="-i" falsevalue="" checked="false" /> - <param name="thinning" type="boolean" label="Additional thinning/scaling down of low quality documents (-j)" truevalue="-j" falsevalue="" checked="false" /> - - </inputs> - <outputs> - <data name="outfile" type="data" format="sdf"> - <change_format> - <when input="oformat" value="can" format="smi"/> - </change_format> - </data> - </outputs> - <tests> - <test> - <param name="infile" ftype="png" value="CID_2244.png"/> - <param name="oformat" value="sdf"/> - <output name="outfile" ftype="sdf" file="osra_on_CID2244.sdf"/> - </test> - <test> - <param name="infile" ftype="png" value="2008001635_153_chem.png"/> - <param name="oformat" value="can"/> - <output name="outfile" ftype="sdf" file="2008001635_153_chem.smi"/> - </test> - - </tests> - <help> - -.. class:: infomark - -**What this tool does** - -OSRA_ (Optical Structure Recognition Application) is a utility designed to convert graphical representations of chemical structures into SMILES or SDF. It generates the SMILES or SDF representation of any molecular structure image within a document which is parseable by GraphicMagick. - -.. _OSRA: http://cactus.nci.nih.gov/osra/ - ------ - -.. class:: infomark - -**Cite** - -Igor V Filippov and Marc C Nicklaus - `Optical Structure Recognition Software To Recover Chemical Information: OSRA, An Open Source Solution`_ - -.. _`Optical Structure Recognition Software To Recover Chemical Information: OSRA, An Open Source Solution`: http://pubs.acs.org/doi/abs/10.1021/ci800067r - </help> -</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/peptide_shaker.xml Fri Apr 11 16:32:28 2014 -0400 @@ -0,0 +1,248 @@ +<tool id="peptide_shaker" name="Peptide Shaker" version="0.1.0"> + <!-- TODO: Set defaults for weights correctly --> + <requirements> + <requirement type="package" version="0.20.1">peptide_shaker</requirement> + <requirement type="package" version="1.14.4">searchgui</requirement> + </requirements> + <description> + Peform protein identification combining X! Tandem and OMSSA (using SearchGUI) and PeptideShaker pipeline. + </description> + <command> + #from datetime import datetime + #set $exp_str = "Galaxy Experiment %s" % datetime.now().strftime("%Y%m%d%H%M%s") + #set $samp_str = "Sample %s" % datetime.now().strftime("%Y%m%d%H%M%s") + mkdir spectra; + mkdir output; + mkdir output_reports; + cwd=`pwd`; + #for $mgf in $peak_lists: + #set $input_name = $mgf.display_name.replace(".mgf", "") + ".mgf" + ln -s '$mgf' 'spectra/$input_name'; + #end for + + java -cp \$SEARCHGUI_JAR_PATH eu.isas.searchgui.cmd.SearchCLI + ##SearchCLI + -spectrum_files \$cwd/spectra + -output_folder \$cwd/output + -ppm $precursor_ion_tol_units + -prec_tol $precursor_ion_tol + -frag_tol $fragment_tol + -enzyme '$enzyme' + #set $fixed_mods_str = $fixed_modifications or '' + #set $variable_mods_str = $variable_modifications or '' + #if $fixed_mods_str + -fixed_mods "$fixed_mods_str" + #end if + #if $variable_mods_str + -variable_mods "$variable_mods_str" + #end if + -mc $missed_cleavages + #if $advanced.specify: + -xtandem $advanced.xtandem + #if $advanced.omssa.run_omssa + #set $omssa = 1 + #else + #set $omssa = 0 + #end if + -omssa $omssa + + #if $omssa == 1 + -hitlist_length ${advanced.omssa.hitlist_length} + -remove_prec ${advanced.omssa.remove_precursor} + -scale_prec ${advanced.omssa.scale_precursor} + -estimate_charge ${advanced.omssa.estimate_charge} + #end if + #end if + -db $input_database; + + + java -cp \$PEPTIDESHAKER_JAR_PATH eu.isas.peptideshaker.cmd.PeptideShakerCLI + ##PeptideShakerCLI + -experiment '$exp_str' + -sample '$samp_str' + -replicate 1 + -spectrum_files \$cwd/spectra + -identification_files \$cwd/output + -search_params \$cwd/output/SearchGUI.parameters + -out_txt_1 \$cwd/output_reports + #if $processing_options.specify + -protein_FDR ${processing_options.protein_fdr} + -peptide_FDR ${processing_options.peptide_fdr} + -psm_FDR ${processing_options.psm_fdr} + -psm_FLR ${processing_options.psm_flr} + #if str($processing_options.a_score.use) == "1" + #set $a_score = 1 + #else + #set $a_score = 0 + #end if + -a_score $a_score + #if str($a_score) == "1" + -a_score_neutral_losses ${processing_options.a_score.neutral_losses} + #end if + #end if + #if $filtering_options.specify + -min_peptide_length ${filtering_options.min_peptide_length} + -max_peptide_length ${filtering_options.max_peptide_length} + -max_precursor_error ${filtering_options.max_precursor_error} + -max_precursor_error_type ${filtering_options.max_precursor_error_type} + -max_xtandem_e ${filtering_options.max_xtandem_e} + -max_omssa_e ${filtering_options.max_omssa_e} + -exclude_unknown_ptms ${filtering_options.exclude_unknown_ptms} + #end if + -out \$cwd/output.cps ; + + mv output_reports/*peptides.txt peptides.txt ; + mv output_reports/*psms.txt psms.txt ; + mv output_reports/*proteins.txt proteins.txt + </command> + <stdio> + <exit_code range="1:" level="fatal" description="Job Failed" /> + </stdio> + <inputs> + <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"/> + <param format="mgf" name="peak_lists" type="data" multiple="true" label="Input Peak Lists (mgf)" + help="Select appropriate MGF dataset(s) from history" /> + <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"> + <option value="1">Parts per million (ppm)</option> + <option value="0">Daltons</option> + </param> + <param name="precursor_ion_tol" type="float" value="10" label="Percursor Ion Tolerance" + help="Provide error value for precursor ion, based on instrument used. 10 ppm recommended for Orbitrap instrument"/> + <param name="fragment_tol" type="float" value="0.5" label="Fragment Tolerance (Daltons)" + help="Provide error value for fragment ions, based on instrument used"/> + <param name="enzyme" type="select" label="Enzyme" + help="Which enzyme was used for protein digest in experiment? In most cases, trypsin is used"> + <option value="Trypsin">Trypsin</option> + <option value="Arg-C">Arg-C</option> + <option value="CNBr">CNBr</option> + <option value="Chymotrypsin (FYWL)">Chymotrypsin (FYWL)</option> + <option value="Formic Acid">Formic Acid</option> + <option value="Lys-C">Lys-C</option> + <option value="Lys-C, no P rule">Lys-C, no P rule</option> + <option value="Pepsin A">Pepsin A</option> + <option value="Trypsin + CNBr">Trypsin + CNBr</option> + <option value="Trypsin + Chymotrypsin (FYWLKR)">Trypsin + Chymotrypsin (FYWLKR)</option> + <option value="Trypsin, no P rule">Trypsin, no P rule</option> + <option value="whole protein">whole protein</option> + <option value="Asp-N">Asp-N</option> + <option value="Glu-C">Glu-C</option> + <option value="Asp-N + Glu-C">Asp-N + Glu-C</option> + <option value="Top-Down">Top-Down</option> + <option value="Semi-Tryptic">Semi-Tryptic</option> + <option value="No enzyme">No enzyme</option> + <option value="Chymotrypsin, no P rule (FYWL)">Chymotrypsin, no P rule (FYWL)</option> + <option value="Asp-N (DE)">Asp-N (DE)</option> + <option value="Glu-C (DE)">Glu-C (DE)</option> + <option value="Lys-N (K)">Lys-N (K)</option> + <option value="Thermolysin, no P rule">Thermolysin, no P rule</option> + <option value="Semi-Chymotrypsin (FYWL)">Semi-Chymotrypsin (FYWL)</option> + <option value="Semi-Glu-C">Semi-Glu-C</option> + </param> + <param name="missed_cleavages" type="integer" value="2" label="Maximum Missed Cleavages" + help="Allow peptides to contain up to this many missed enzyme cleavage sites. 2 is the recommended value"/> + <param name="fixed_modifications" type="select" label="Fixed Modifications" multiple="true" + help="Occurs in known places on peptide sequence. Hold the appropriate key while clicking to select multiple items"> + <options from_file="searchgui_mods.loc"> + <column name="name" index="0" /> + <column name="value" index="0" /> + </options> + </param> + <param name="variable_modifications" type="select" label="Variable Modifications" multiple="true" + help="Can occur anywhere on the peptide sequence; adds additional error to search score. Hold the appropriate key while clicking to select multiple items"> + <options from_file="searchgui_mods.loc"> + <column name="name" index="0" /> + <column name="value" index="0" /> + </options> + </param> + <param name="min_charge" label="Minimum Charge" value="2" type="integer" help="Lowest searched charge value for fragment ions"/> + <param name="max_charge" label="Maximum Charge" value="4" type="integer" help="Highest searched charge value for fragment ions"/> + <param name="forward_ion" label="Forward Ion" type="select" help="Searched fragment ion type. Select a, b or c based on collisions induced in experiment"> + <option value="a">a</option> + <option value="b" selected="true">b</option> + <option value="c">c</option> + </param> + <param name="reverse_ion" label="Reverse Ion" type="select" help="Searched fragment ion type. Select x, y, or z based on collisions induced in experiment"> + <option value="x">x</option> + <option value="y" selected="true">y</option> + <option value="z">z</option> + </param> + <conditional name="advanced"> + <param name="specify" label="Specify Advanced Search Options" type="boolean" truevalue="true" falsevalue="false" + help=" Run X! Tandem, OMSSA, or both and provide options for OMSSA search"/> + <when value="false" /> + <when value="true"> + <param name="xtandem" label="Run X! Tandem" type="boolean" truevalue="1" falsevalue="0" checked="true" /> + <conditional name="omssa"> + <param name="run_omssa" label="Run OMSSA" type="boolean" truevalue="1" falsevalue="0" checked="true" /> + <when value="0" /> + <when value="1"> + <param name="hitlist_length" label="OMSSA: Hit List Length" type="integer" value="25" /> + <param name="remove_precursor" label="OMSSA: Remove Precurosr" type="boolean" truevalue="1" falsevalue="0" checked="true"/> + <param name="scale_precursor" label="OMSSA: Scale Precursor Mass" type="boolean" truevalue="1" falsevalue="0" checked="false"/> + <param name="estimate_charge" label="OMSSA: Estimate Charge" type="boolean" truevalue="1" falsevalue="0" checked="true" /> + </when> + </conditional> + </when> + </conditional> + <conditional name="processing_options"> + <param name="specify" label="Specify Advanced PeptideShaker Processing Options" type="boolean" truevalue="true" falsevalue="false" + help="Select and provide False Discovery Rate (FDR) levels at the peptide, protein, + and peptide-spectral match (PSM) levels, as well as False Loss Rate (FLR) for PSM’s and A score options for post-translational modifications (PTM’s). See this link_ for more details + .. _link: http://peptide-shaker.googlecode.com/svn-history/r1267/wiki/tutorial/6_ptm_analysis.docx" /> + <when value="false" /> + <when value="true"> + <param name="protein_fdr" label="FDR at the protein level" help="In percent (default 1% FDR: '1')" value="1" type="float" /> + <param name="peptide_fdr" label="FDR at the peptide level" help="In percent (default 1% FDR: '1')" value="1" type="float" /> + <param name="psm_fdr" label="FDR at the PSM level" help="In percent (default 1% FDR: '1')" value="1" type="float" /> + <param name="psm_flr" label="FLR at the PSM level" value="1" type="float" + help="In percent (default 1% FLR: '1'). Percent for peptides with different potential modification sites and one variable modification." /> + <conditional name="a_score"> + <param name="use" label="Calculate A Score" type="boolean" truevalue="1" falsevalue="0" checked="true" /> + <when value="0" /> + <when value="1"> + <param name="neutral_losses" label="Include Neutral Losses in A Score" type="boolean" truevalue="1" falsevalue="0" /> + </when> + </conditional> + <!-- SKIPPING -protein_fraction_mw_confidence ${processing_options.protein_fraction_mw_confidence} --> + </when> + </conditional> + <conditional name="filtering_options"> + <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’s"/> + <when value="false" /> + <when value="true"> + <param name="min_peptide_length" label="Minimum Peptide Length" value="6" type="integer" /> + <param name="max_peptide_length" label="Maximum Peptide Length" value="30" type="integer" /> + <param name="max_precursor_error" label="Maximum Precursor Error" value="10" type="float" help="Next option specifies units (Da or ppm)." /> + <param name="max_precursor_error_type" label="Maximum Precursor Error Type" type="select"> + <option value="0">ppm</option> + <option value="1">Daltons</option> + </param> + <param name="max_xtandem_e" label="Maximum X! Tandem E Value" value="100" type="float" help="" /> + <param name="max_omssa_e" label="Maximum OMSSA E Value" value="100" type="float" help="" /> + <param name="exclude_unknown_ptms" label="Exclude Unknown PTMs" type="boolean" truevalue="1" falsevalue="0" checked="true" /> + </when> + </conditional> + </inputs> + <outputs> + <data format="cps" name="output" from_work_dir="output.cps" label="PeptideShaker CPS results for ${on_string}" /> + <data format="tabular" name="output_peptides" from_work_dir="peptides.txt" label="PeptideShaker Peptide Report for ${on_string}" /> + <data format="tabular" name="output_proteins" from_work_dir="proteins.txt" label="PeptideShaker Protein Report for ${on_string}" /> + <data format="tabular" name="output_psms" from_work_dir="psms.txt" label="PeptideShaker PSM Report for ${on_string}" /> + </outputs> + <help> +**What it does** + +Runs multiple search engines (X! Tandem and OMSSA) on any number of MGF peak lists using the SearchGUI application and combines the results. + +------ + +**Citation** + +For the underlying tool, please cite `TODO` + +If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/peptideshaker + </help> +</tool>
--- a/readme Thu Apr 03 06:07:32 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,20 +0,0 @@ -OSRA: Optical Structure Recognition Application - -OSRA is a utility designed to convert graphical representations of chemical -structures, as they appear in journal articles, patent documents, textbooks, -trade magazines etc., into SMILES (Simplified Molecular Input Line Entry -Specification - see http://en.wikipedia.org/wiki/SMILES) or -SD files - a computer recognizable molecular structure format. -OSRA can read a document in any of the over 90 graphical formats parseable by -ImageMagick - including GIF, JPEG, PNG, TIFF, PDF, PS etc., and generate -the SMILES or SDF representation of the molecular structure images encountered -within that document. - -Note that any software designed for optical recognition is unlikely to be -perfect, and the output produced might, and probably will, contain errors, -so curation by a human knowledgeable in chemical structures is highly recommended. - -http://cactus.nci.nih.gov/osra/ - -The wrapper comes with an automatic installation of all dependencies through the -galaxy toolshed.
--- a/repository_dependencies.xml Thu Apr 03 06:07:32 2014 -0400 +++ b/repository_dependencies.xml Fri Apr 11 16:32:28 2014 -0400 @@ -1,4 +1,4 @@ <?xml version="1.0"?> -<repositories description="This requires the Molecule datatype definitions (e.g. SMILES, InChI, SD-format)."> - <repository changeset_revision="8714f927a6ee" name="molecule_datatypes" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" /> +<repositories description="Required proteomics dependencies."> + <repository changeset_revision="25f42af5b73d" name="proteomics_datatypes" owner="iracooke" toolshed="http://testtoolshed.g2.bx.psu.edu" /> </repositories>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/reverse.py Fri Apr 11 16:32:28 2014 -0400 @@ -0,0 +1,50 @@ +#!/usr/bin/env python +from os.path import join +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( args.script_path ) + _exec("%s %s %s" % (command_prefix, java_class, args)) + + +def _dbtoolkit_jar_path( script_path ): + jar_path = join(script_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") + parser.add_option("-s", "--script_path") + return parser.parse_args() + + +if __name__ == "__main__": + main()
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/reverse.xml Fri Apr 11 16:32:28 2014 -0400 @@ -0,0 +1,33 @@ +<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> + <requirement type="set_environment">PEPTIDESHAKER_SCRIPT_PATH</requirement> + </requirements> + <command interpreter="python"> + reverse.py + --input='$input' + --output='$output' + --script_path \$PEPTIDESHAKER_SCRIPT_PATH + </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/peptideshaker . + + </help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/searchgui_mods.loc.sample Fri Apr 11 16:32:28 2014 -0400 @@ -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
--- a/test_data/2008001635_153_chem.smi Thu Apr 03 06:07:32 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -CCC(c1ccc(cc1)Br)OCCCO
--- a/test_data/CID_2244.sdf Thu Apr 03 06:07:32 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,155 +0,0 @@ -2244 - -OEChem-05151212332D - - 21 21 0 0 0 0 0 0 0999 V2000 - 3.7320 -0.0600 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 - 6.3301 1.4400 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 - 4.5981 1.4400 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 - 2.8660 -1.5600 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 - 4.5981 -0.5600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 5.4641 -0.0600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 4.5981 -1.5600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 6.3301 -0.5600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 5.4641 -2.0600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 6.3301 -1.5600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 5.4641 0.9400 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 2.8660 -0.5600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 2.0000 -0.0600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 4.0611 -1.8700 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 - 6.8671 -0.2500 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 - 5.4641 -2.6800 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 - 6.8671 -1.8700 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 - 2.3100 0.4769 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 - 1.4631 0.2500 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 - 1.6900 -0.5969 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 - 6.3301 2.0600 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 - 1 5 1 0 0 0 0 - 1 12 1 0 0 0 0 - 2 11 1 0 0 0 0 - 2 21 1 0 0 0 0 - 3 11 2 0 0 0 0 - 4 12 2 0 0 0 0 - 5 6 1 0 0 0 0 - 5 7 2 0 0 0 0 - 6 8 2 0 0 0 0 - 6 11 1 0 0 0 0 - 7 9 1 0 0 0 0 - 7 14 1 0 0 0 0 - 8 10 1 0 0 0 0 - 8 15 1 0 0 0 0 - 9 10 2 0 0 0 0 - 9 16 1 0 0 0 0 - 10 17 1 0 0 0 0 - 12 13 1 0 0 0 0 - 13 18 1 0 0 0 0 - 13 19 1 0 0 0 0 - 13 20 1 0 0 0 0 -M END -> <PUBCHEM_COMPOUND_CID> -2244 - -> <PUBCHEM_COMPOUND_CANONICALIZED> -1 - -> <PUBCHEM_CACTVS_COMPLEXITY> -212 - -> <PUBCHEM_CACTVS_HBOND_ACCEPTOR> -4 - -> <PUBCHEM_CACTVS_HBOND_DONOR> -1 - -> <PUBCHEM_CACTVS_ROTATABLE_BOND> -3 - -> <PUBCHEM_CACTVS_SUBSKEYS> -AAADccBwOAAAAAAAAAAAAAAAAAAAAAAAAAAwAAAAAAAAAAABAAAAGgAACAAADASAmAAyDoAABgCIAiDSCAACCAAkIAAIiAEGCMgMJzaENRqCe2Cl4BEIuYeIyCCOAAAAAAAIAAAAAAAAABAAAAAAAAAAAA== - -> <PUBCHEM_IUPAC_OPENEYE_NAME> -2-acetoxybenzoic acid - -> <PUBCHEM_IUPAC_CAS_NAME> -2-acetyloxybenzoic acid - -> <PUBCHEM_IUPAC_NAME> -2-acetyloxybenzoic acid - -> <PUBCHEM_IUPAC_SYSTEMATIC_NAME> -2-acetyloxybenzoic acid - -> <PUBCHEM_IUPAC_TRADITIONAL_NAME> -2-acetoxybenzoic acid - -> <PUBCHEM_IUPAC_INCHI> -InChI=1S/C9H8O4/c1-6(10)13-8-5-3-2-4-7(8)9(11)12/h2-5H,1H3,(H,11,12) - -> <PUBCHEM_IUPAC_INCHIKEY> -BSYNRYMUTXBXSQ-UHFFFAOYSA-N - -> <PUBCHEM_XLOGP3> -1.2 - -> <PUBCHEM_EXACT_MASS> -180.042259 - -> <PUBCHEM_MOLECULAR_FORMULA> -C9H8O4 - -> <PUBCHEM_MOLECULAR_WEIGHT> -180.15742 - -> <PUBCHEM_OPENEYE_CAN_SMILES> -CC(=O)OC1=CC=CC=C1C(=O)O - -> <PUBCHEM_OPENEYE_ISO_SMILES> -CC(=O)OC1=CC=CC=C1C(=O)O - -> <PUBCHEM_CACTVS_TPSA> -63.6 - -> <PUBCHEM_MONOISOTOPIC_WEIGHT> -180.042259 - -> <PUBCHEM_TOTAL_CHARGE> -0 - -> <PUBCHEM_HEAVY_ATOM_COUNT> -13 - -> <PUBCHEM_ATOM_DEF_STEREO_COUNT> -0 - -> <PUBCHEM_ATOM_UDEF_STEREO_COUNT> -0 - -> <PUBCHEM_BOND_DEF_STEREO_COUNT> -0 - -> <PUBCHEM_BOND_UDEF_STEREO_COUNT> -0 - -> <PUBCHEM_ISOTOPIC_ATOM_COUNT> -0 - -> <PUBCHEM_COMPONENT_COUNT> -1 - -> <PUBCHEM_CACTVS_TAUTO_COUNT> -1 - -> <PUBCHEM_COORDINATE_TYPE> -1 -5 -255 - -> <PUBCHEM_BONDANNOTATIONS> -5 6 8 -5 7 8 -6 8 8 -7 9 8 -8 10 8 -9 10 8 - -$$$$ -
--- a/tool_dependencies.xml Thu Apr 03 06:07:32 2014 -0400 +++ b/tool_dependencies.xml Fri Apr 11 16:32:28 2014 -0400 @@ -1,74 +1,12 @@ <?xml version="1.0"?> <tool_dependency> - <package name="openbabel" version="2.3.2"> - <repository changeset_revision="8426be5149ce" name="package_openbabel_2_3" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" /> - </package> - <package name="graphicsmagick" version="1.3.18"> - <repository changeset_revision="2fd4eb971ba5" name="package_graphicsmagick_1_3" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" /> + <set_environment version="1.0"> + <environment_variable action="set_to" name="PEPTIDESHAKER_SCRIPT_PATH">$REPOSITORY_INSTALL_DIR</environment_variable> + </set_environment> + <package name="searchgui" version="1.14.1"> + <repository changeset_revision="0692ca995a01" name="package_searchgui_1_14_4" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" /> </package> - <package name="osra" version="2.0.0"> - <install version="1.0"> - <actions> - <!-- first action is always downloading --> - <action type="download_by_url">http://downloads.sourceforge.net/project/osra/osra/2.0.0/osra-2.0.0.tgz</action> - - <!-- populate the environment variables from the dependend repos --> - <action type="set_environment_for_install"> - <repository changeset_revision="8426be5149ce" name="package_openbabel_2_3" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu"> - <package name="openbabel" version="2.3.2" /> - </repository> - <repository changeset_revision="2fd4eb971ba5" name="package_graphicsmagick_1_3" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu"> - <package name="graphicsmagick" version="1.3.18" /> - </repository> - </action> - - <!--compiling potrace-1.11 --> - <action type="shell_command">wget http://potrace.sourceforge.net/download/potrace-1.11.tar.gz</action> - <action type="shell_command">tar xfvz potrace-1.11.tar.gz && cd potrace-1.11 && ./configure --with-libpotrace --prefix=$INSTALL_DIR/potrace/build && make && make install</action> - - <!--compiling gocr 0.50patched --> - <!-- not yet possible - <action type="shell_command">wget http://www-e.uni-magdeburg.de/jschulen/ocr/gocr-0.50.tar.gz</action> - <action type="shell_command">tar xfvz gocr-0.50.tar.gz && cd gocr-0.50 && ./configure -|-prefix=$INSTALL_DIR/gocr/build && make libs && make all install</action> - --> - <action type="shell_command">wget http://downloads.sourceforge.net/project/osra/gocr-patched/gocr-0.50pre-patched.tgz</action> - <action type="shell_command">tar xfvz gocr-0.50pre-patched.tgz && cd gocr-0.50pre-patched && ./configure --prefix=$INSTALL_DIR/gocr/build && make libs && make all install</action> - - - <!--compiling tclap 1.2.1 --> - <action type="shell_command">wget http://downloads.sourceforge.net/project/tclap/tclap-1.2.1.tar.gz</action> - <action type="shell_command">tar xfvz tclap-1.2.1.tar.gz && cd tclap-1.2.1 && ./configure --prefix=$INSTALL_DIR/tclap/build && make && make install</action> - - <!--compiling ocrad 0.21 --> - <action type="shell_command">wget http://mirror.checkdomain.de/gnu/ocrad/ocrad-0.21.tar.gz</action> - <action type="shell_command">tar xfvz ocrad-0.21.tar.gz && cd ocrad-0.21 && ./configure --prefix=$INSTALL_DIR/ocrad/build && make && make install</action> - - <!--compiling cuneiform 1.1.0 --> - <action type="shell_command">wget https://launchpad.net/cuneiform-linux/1.1/1.1/+download/cuneiform-linux-1.1.0.tar.bz2</action> - <action type="shell_command">tar xfvj cuneiform-linux-1.1.0.tar.bz2 && cd cuneiform-linux-1.1.0 && mkdir build && cd build && cmake .. -DCMAKE_INSTALL_PREFIX=$INSTALL_DIR/cuneiform/build/ && make && make install</action> - - <!--And finally OSRA 1.4.0--> - <!-- Extending the PATH is needed for OSRA --> - <action type="shell_command">export PATH=$PATH:$GRAPHICSMAGICK_ROOT_DIR/bin/ && - ./configure --with-tclap-include=$INSTALL_DIR/tclap/build/include/ --with-potrace-include=$INSTALL_DIR/potrace/build/include/ --with-potrace-lib=$INSTALL_DIR/potrace/build/lib/ --with-gocr-include=$INSTALL_DIR/gocr/build/include/gocr/ --with-gocr-lib=$INSTALL_DIR/gocr/build/lib/ --with-ocrad-include=$INSTALL_DIR/ocrad/build/include/ --with-ocrad-lib=$INSTALL_DIR/ocrad/build/lib/ --with-cuneiform-include=$INSTALL_DIR/cuneiform/build/install/include/ --with-cuneiform --with-cuneiform-lib=$INSTALL_DIR/cuneiform/build/install/lib/ --with-openbabel-include=$OPENBABEL_INCLUDE_DIR/openbabel-2.0/ --with-openbabel-lib=$OPENBABEL_LIB_DIR --with-graphicsmagick-lib=$GRAPHICSMAGICK_ROOT_DIR/lib/ --with-graphicsmagick-include=$GRAPHICSMAGICK_ROOT_DIR/include/GraphicsMagick/ --prefix=$INSTALL_DIR </action> - <action type="shell_command">make</action> - <action type="shell_command">make install</action> - - <action type="shell_command">rm $INSTALL_DIR/tclap/ -r</action> - <!--<action type="shell_command">rm $INSTALL_DIR/openbabel/ -r</action>--> - <action type="shell_command">rm $INSTALL_DIR/gocr/ -r</action> - <action type="shell_command">rm $INSTALL_DIR/ocrad/ -r</action> - <action type="shell_command">rm $INSTALL_DIR/cuneiform/ -r</action> - - <action type="set_environment"> - <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$ENV[GRAPHICSMAGICK_ROOT_DIR]/lib/</environment_variable> - <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$INSTALL_DIR/potrace/build/lib/</environment_variable> - <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> - <!-- OSRA_DATA_FILES is only used by the galaxy wrapper and is not part of OSRA --> - <environment_variable action="set_to" name="OSRA_DATA_FILES">$INSTALL_DIR/share</environment_variable> - </action> - </actions> - </install> - <readme>We still have a handfull of requirements</readme> + <package name="peptide_shaker" version="0.20.1"> + <repository changeset_revision="c661fad47f03" name="package_peptideshaker_0_20_1" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" /> </package> </tool_dependency>