Mercurial > repos > galaxyp > peptideshaker
changeset 2:fb591fc7241c draft
Improved some datatype handling
| author | galaxyp |
|---|---|
| date | Thu, 20 Jun 2013 11:02:36 -0400 |
| parents | 7a74818e0eeb |
| children | 679a4b0041a4 |
| files | 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 galaxyp-toolshed-peptideshaker peptide_shaker.xml peptideshaker.py reverse.py reverse.xml |
| diffstat | 11 files changed, 309 insertions(+), 1491 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/datatypes_conf.xml Thu Jun 20 11:02:36 2013 -0400 @@ -0,0 +1,9 @@ +<?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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We're also free for small teams! - - </p> - <a class="aui-button aui-button-primary aui-style signup-button" href="/account/signup/">Sign up for free</a> - <span class="close aui-icon aui-icon-small aui-iconfont-close-dialog" title="Dismiss this banner">Close</span> - </div> -</section> - - - - - - <section id="readme"> - - <article class="readme file"> - <p>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.</p> -<p>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.</p> -<p>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.</p> -<p>Also, PeptideShaker may require xvfb to simulate an X environment if -this is installed on a headless server.</p> -<h1 id="markdown-header-obtaining-tools">Obtaining Tools</h1> -<p>Repositories for all Galaxy-P tools can be found at -https:/bitbucket.org/galaxyp/.</p> -<h1 id="markdown-header-contact">Contact</h1> -<p>Please send suggestions for improvements and bug reports to -jmchilton@gmail.com.</p> -<h1 id="markdown-header-license">License</h1> -<p>All Galaxy-P tools are licensed under the Apache License Version 2.0 -unless otherwise documented.</p> -<h1 id="markdown-header-tool-versioning">Tool Versioning</h1> -<p>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.</p> - </article> - - </section> - - - - <section id="repo-activity"> - <h1> - Recent activity - <a href="/galaxyp/galaxyp-toolshed-peptideshaker/rss" class="icon rss">RSS feed fo galaxyp-toolshed-peptideshaker</a> - </h1> - - - - - - - - - -<div class="newsfeed"> - - - - - - - - - - - - <article class="news-item commit"> - <span class="icon commit"></span> - - - - <a href="/galaxyp"><img alt="galaxyp" src="https://secure.gravatar.com/avatar/655358b258b3fbd64aa5c6f42adade4e?d=https%3A%2F%2Fd3oaxc4q5k2d6q.cloudfront.net%2Fm%2F968d9745b7be%2Fimg%2Fdefault_team_avatar%2F32%2Fteam_blue.png&s=32" class="avatar avatar32" /></a> - - - <p> - - - <a href="/galaxyp">galaxyp</a> - - pushed 1 commit to - - -<a href="/galaxyp/galaxyp-toolshed-peptideshaker" title="galaxyp/galaxyp-toolshed-peptideshaker">galaxyp/galaxyp-toolshed-peptideshaker</a> - - - </p> - <time datetime="2013-06-19T22:19:56+00:00">16 hours ago</time> - - <div class="changeset"> - <a href="/galaxyp/galaxyp-toolshed-peptideshaker/commits/80ef7cf0d97a14a59b39f2d7eb683531cc02056a" class="changeset-hash">80ef7cf</a> - - - - - improved some datatypes - - - </div> - - - </article> - - - - - - - - - - - - - - - - </article> - - - - - - - <article class="news-item commit"> - <span class="icon commit"></span> - - - - <a href="/jmchilton"><img alt="John Chilton" src="https://secure.gravatar.com/avatar/86cbb595c758989c14ae715c44588998?d=https%3A%2F%2Fd3oaxc4q5k2d6q.cloudfront.net%2Fm%2F968d9745b7be%2Fimg%2Fdefault_avatar%2F32%2Fuser_blue.png&s=32" class="avatar avatar32" /></a> - - - <p> - - - <a href="/jmchilton">John Chilton</a> - - pushed 1 commit to - - -<a href="/galaxyp/galaxyp-toolshed-peptideshaker" title="galaxyp/galaxyp-toolshed-peptideshaker">galaxyp/galaxyp-toolshed-peptideshaker</a> - - - </p> - <time datetime="2013-06-07T03:03:07+00:00">2013-06-07</time> - - <div class="changeset"> - <a href="/galaxyp/galaxyp-toolshed-peptideshaker/commits/113acce8b7eea4ed179411f6704ab5a5d8245da8" class="changeset-hash">113acce</a> - - - - - Ensure unique Experiment/Sample names. Peptideshaker seems to potentially have clean up problem on errors otherwise. - - - </div> - - - </article> - - - - - - - - - - - - - - - - - - - <article class="news-item commit"> - <span class="icon commit"></span> - - - - <a href="/jmchilton"><img alt="John Chilton" src="https://secure.gravatar.com/avatar/86cbb595c758989c14ae715c44588998?d=https%3A%2F%2Fd3oaxc4q5k2d6q.cloudfront.net%2Fm%2F968d9745b7be%2Fimg%2Fdefault_avatar%2F32%2Fuser_blue.png&s=32" class="avatar avatar32" /></a> - - - <p> - - - <a href="/jmchilton">John Chilton</a> - - pushed 1 commit to - - -<a href="/galaxyp/galaxyp-toolshed-peptideshaker" title="galaxyp/galaxyp-toolshed-peptideshaker">galaxyp/galaxyp-toolshed-peptideshaker</a> - - - </p> - <time datetime="2013-05-20T15:26:48+00:00">2013-05-20</time> - - <div class="changeset"> - <a href="/galaxyp/galaxyp-toolshed-peptideshaker/commits/6fa4a7ad242f1ce78db6eaec19099bd1b7f86b2f" class="changeset-hash">6fa4a7a</a> - - - - - Add script to create a target-decoy database for PeptideShaker - seems very picky about the format of the database. - - - </div> - - - </article> - - - - - - - - - - - - - - - - - - - <article class="news-item commit"> - <span class="icon commit"></span> - - - - <a href="/jmchilton"><img alt="John Chilton" src="https://secure.gravatar.com/avatar/86cbb595c758989c14ae715c44588998?d=https%3A%2F%2Fd3oaxc4q5k2d6q.cloudfront.net%2Fm%2F968d9745b7be%2Fimg%2Fdefault_avatar%2F32%2Fuser_blue.png&s=32" class="avatar avatar32" /></a> - - - <p> - - - <a href="/jmchilton">John Chilton</a> - - pushed 2 commits to - - -<a href="/galaxyp/galaxyp-toolshed-peptideshaker" title="galaxyp/galaxyp-toolshed-peptideshaker">galaxyp/galaxyp-toolshed-peptideshaker</a> - - - </p> - <time datetime="2013-05-13T18:51:02+00:00">2013-05-13</time> - - <div class="changeset"> - <a href="/galaxyp/galaxyp-toolshed-peptideshaker/commits/bf3730228118ac8adee5e5fc16f08ad5f9aaaf0e" class="changeset-hash">bf37302</a> - - - - - Add CPS datatype. - - - </div> - - <div class="changeset"> - <a href="/galaxyp/galaxyp-toolshed-peptideshaker/commits/d63d2ed28d002156d5330d29afbf8afc54adfc3b" class="changeset-hash">d63d2ed</a> - - - - - Improve documentation. - - - </div> - - - </article> - - - - - - - - - - - - - - - - - - - <article class="news-item commit"> - <span class="icon commit"></span> - - - - <a href="/jmchilton"><img alt="John Chilton" src="https://secure.gravatar.com/avatar/86cbb595c758989c14ae715c44588998?d=https%3A%2F%2Fd3oaxc4q5k2d6q.cloudfront.net%2Fm%2F968d9745b7be%2Fimg%2Fdefault_avatar%2F32%2Fuser_blue.png&s=32" class="avatar avatar32" /></a> - - - <p> - - - <a href="/jmchilton">John Chilton</a> - - pushed 1 commit to - - -<a href="/galaxyp/galaxyp-toolshed-peptideshaker" title="galaxyp/galaxyp-toolshed-peptideshaker">galaxyp/galaxyp-toolshed-peptideshaker</a> - - - </p> - <time datetime="2013-05-10T21:39:19+00:00">2013-05-10</time> - - <div class="changeset"> - <a href="/galaxyp/galaxyp-toolshed-peptideshaker/commits/a76da3b08725332a9dc746b3f4e886d047af2e40" class="changeset-hash">a76da3b</a> - - - - - Add license and documentation. - - - </div> - - - </article> - - - - - - - - - - - - - - - - - - - <article class="news-item commit"> - <span class="icon commit"></span> - - - - <a href="/jmchilton"><img alt="John Chilton" src="https://secure.gravatar.com/avatar/86cbb595c758989c14ae715c44588998?d=https%3A%2F%2Fd3oaxc4q5k2d6q.cloudfront.net%2Fm%2F968d9745b7be%2Fimg%2Fdefault_avatar%2F32%2Fuser_blue.png&s=32" class="avatar avatar32" /></a> - - - <p> - - - <a href="/jmchilton">John Chilton</a> - - pushed 1 commit to - - -<a href="/galaxyp/galaxyp-toolshed-peptideshaker" title="galaxyp/galaxyp-toolshed-peptideshaker">galaxyp/galaxyp-toolshed-peptideshaker</a> - - - </p> - <time datetime="2013-05-10T21:33:27+00:00">2013-05-10</time> - - <div class="changeset"> - <a href="/galaxyp/galaxyp-toolshed-peptideshaker/commits/29ee7c62dfdc24848cc1111500d544c700ca9008" class="changeset-hash">29ee7c6</a> - - - - - Add sample loc file for toolshed. - - - </div> - - - </article> - - - - - - - - - - - - - - - - - - - <article class="news-item commit"> - <span class="icon commit"></span> - - - - <a href="/jmchilton"><img alt="John Chilton" src="https://secure.gravatar.com/avatar/86cbb595c758989c14ae715c44588998?d=https%3A%2F%2Fd3oaxc4q5k2d6q.cloudfront.net%2Fm%2F968d9745b7be%2Fimg%2Fdefault_avatar%2F32%2Fuser_blue.png&s=32" class="avatar avatar32" /></a> - - - <p> - - - <a href="/jmchilton">John Chilton</a> - - pushed 1 commit to - - -<a href="/galaxyp/galaxyp-toolshed-peptideshaker" title="galaxyp/galaxyp-toolshed-peptideshaker">galaxyp/galaxyp-toolshed-peptideshaker</a> - - - </p> - <time datetime="2013-04-12T18:58:24+00:00">2013-04-12</time> - - <div class="changeset"> - <a href="/galaxyp/galaxyp-toolshed-peptideshaker/commits/8384b7acd805161da0b61203688c61ed0b11b72b" class="changeset-hash">8384b7a</a> - - - - - Fix modification handling. - - - </div> - - - </article> - - - - - - - - - - - - - - - - - - - <article class="news-item commit"> - <span class="icon commit"></span> - - - - <a href="/jmchilton"><img alt="John Chilton" src="https://secure.gravatar.com/avatar/86cbb595c758989c14ae715c44588998?d=https%3A%2F%2Fd3oaxc4q5k2d6q.cloudfront.net%2Fm%2F968d9745b7be%2Fimg%2Fdefault_avatar%2F32%2Fuser_blue.png&s=32" class="avatar avatar32" /></a> - - - <p> - - - <a href="/jmchilton">John Chilton</a> - - pushed 1 commit to - - -<a href="/galaxyp/galaxyp-toolshed-peptideshaker" title="galaxyp/galaxyp-toolshed-peptideshaker">galaxyp/galaxyp-toolshed-peptideshaker</a> - - - </p> - <time datetime="2013-04-11T18:38:44+00:00">2013-04-11</time> - - <div class="changeset"> - <a href="/galaxyp/galaxyp-toolshed-peptideshaker/commits/735b677030185833e6dee7a38e37a0b8ef49a2fb" class="changeset-hash">735b677</a> - - - - - PeptideShaker modifications need to be all lower case. - - - </div> - - - </article> - - - - - - - - - - - - - - - - - - - <article class="news-item commit"> - <span class="icon commit"></span> - - - - <a href="/jmchilton"><img alt="John Chilton" src="https://secure.gravatar.com/avatar/86cbb595c758989c14ae715c44588998?d=https%3A%2F%2Fd3oaxc4q5k2d6q.cloudfront.net%2Fm%2F968d9745b7be%2Fimg%2Fdefault_avatar%2F32%2Fuser_blue.png&s=32" class="avatar avatar32" /></a> - - - <p> - - - <a href="/jmchilton">John Chilton</a> - - pushed 2 commits to - - -<a href="/galaxyp/galaxyp-toolshed-peptideshaker" title="galaxyp/galaxyp-toolshed-peptideshaker">galaxyp/galaxyp-toolshed-peptideshaker</a> - - - </p> - <time datetime="2013-04-08T19:54:06+00:00">2013-04-08</time> - - <div class="changeset"> - <a href="/galaxyp/galaxyp-toolshed-peptideshaker/commits/1f4e30851033eb83986c2d793ba894604f9fe1b0" class="changeset-hash">1f4e308</a> - - - - - Implement modifications for peptide_shaker wrapper. - - - </div> - - <div class="changeset"> - <a href="/galaxyp/galaxyp-toolshed-peptideshaker/commits/90c86636c57d28ba6f369e0e0d1aa097c46f5d4b" class="changeset-hash">90c8663</a> - - - - - Initial work on building modification list for searchGUI. - - - </div> - - - </article> - - - - - - - - - - - - - - - - - - - <article class="news-item commit"> - <span class="icon commit"></span> - - - - <a href="/jmchilton"><img alt="John Chilton" src="https://secure.gravatar.com/avatar/86cbb595c758989c14ae715c44588998?d=https%3A%2F%2Fd3oaxc4q5k2d6q.cloudfront.net%2Fm%2F968d9745b7be%2Fimg%2Fdefault_avatar%2F32%2Fuser_blue.png&s=32" class="avatar avatar32" /></a> - - - <p> - - - <a href="/jmchilton">John Chilton</a> - - pushed 1 commit to - - -<a href="/galaxyp/galaxyp-toolshed-peptideshaker" title="galaxyp/galaxyp-toolshed-peptideshaker">galaxyp/galaxyp-toolshed-peptideshaker</a> - - - </p> - <time datetime="2013-03-19T19:23:06+00:00">2013-03-19</time> - - <div class="changeset"> - <a href="/galaxyp/galaxyp-toolshed-peptideshaker/commits/21b540795f0663a4633a53c78d733746a463167d" class="changeset-hash">21b5407</a> - - - - - Fix label on protein report. - - - </div> - - - </article> - - - - - - - </article> - - - - - -</div> - - - - - - - </section> - </div> - - <div class="column"> - - - - - <section id="repo-stats"> - -<div class="clone-url"> - <div class="aui-buttons"> - <a href="https://bitbucket.org/galaxyp/galaxyp-toolshed-peptideshaker" - class="aui-button aui-style aui-dropdown2-trigger" aria-haspopup="true" - aria-owns="clone-url-dropdown-overview"> - <span class="dropdown-text">HTTPS</span> - </a> - <div id="clone-url-dropdown-overview" class="aui-dropdown2 aui-style-default"> - 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--- a/peptide_shaker.xml Thu Jun 20 10:53:16 2013 -0400 +++ b/peptide_shaker.xml Thu Jun 20 11:02:36 2013 -0400 @@ -4,6 +4,9 @@ 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; @@ -45,8 +48,8 @@ #end if -db $input_database; PeptideShakerCLI \ - -experiment 'Galaxy Experiment' \ - -sample 'Sample' \ + -experiment '$exp_str' \ + -sample '$samp_str' \ -replicate 1 \ -spectrum_files \$cwd/spectra \ -identification_files \$cwd/output \ @@ -210,12 +213,14 @@ <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 result via PeptideShaker. + ------ **Citation** For the underlying tool, please cite `TODO` -If you use this tool in Galaxy, please cite TODO +If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-peptideshaker </help> </tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/peptideshaker.py Thu Jun 20 11:02:36 2013 -0400 @@ -0,0 +1,8 @@ +from galaxy.datatypes.binary import Binary + + +class Cps(Binary): + """Class describing a PeptideShaker CPS files""" + file_ext = "cps" + +Binary.register_unsniffable_binary_ext('cps')
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/reverse.py Thu Jun 20 11:02:36 2013 -0400 @@ -0,0 +1,50 @@ +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()
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/reverse.xml Thu Jun 20 11:02:36 2013 -0400 @@ -0,0 +1,32 @@ +<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>