Mercurial > repos > bgruening > peptideshaker
changeset 39:1e9db1e7fdcd draft
planemo upload commit bd558dfd8243ad3507f95f9dd130dc4011f934c3-dirty
| author | iracooke |
|---|---|
| date | Mon, 04 May 2015 20:25:30 -0400 |
| parents | b6f4f4689f5f |
| children | d5e9a31de022 |
| files | README.md README.rst peptide_shaker.xml searchgui.xml tool_dependencies.xml |
| diffstat | 5 files changed, 110 insertions(+), 106 deletions(-) [+] |
line wrap: on
line diff
--- a/README.md Tue Mar 24 19:58:38 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,72 +0,0 @@ -GalaxyP - PeptideShaker -======================= - -* Home: <https://github.com/galaxyproteomics/tools-galaxyp/> -* Galaxy Tool Shed: <http://toolshed.g2.bx.psu.edu/view/galaxyp/peptideshaker> -* Tool ID: `peptideshaker`, `search_gui` - - -Description ------------ - -Perform 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. - - -Configuration -------------- - -This tool requires a Java runtime 1.6 or greater to work. To avoid out of memory errors you should set the maximum heapspace for java processes as the default is most likely too small. For example, to set this in your shell: - - export _JAVA_OPTIONS='-Xmx1500M' - -It is also possible to set this on a per tool basis using advanced features of the galaxy job config system. - -Note: - -- 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://github.com/galaxyproteomics/) and other information can be found at: - -<https://github.com/galaxyproteomics> - - -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://github.com/galaxyproteomics/tools-galaxyp/> - - -Authors -------- - -Authors and contributors: - -* Bjoern Gruening <bjoern.gruening@gmail.com> -* Ira Cooke -* 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/README.rst Mon May 04 20:25:30 2015 -0400 @@ -0,0 +1,78 @@ +GalaxyP - PeptideShaker +======================= + +- Home: <https://github.com/galaxyproteomics/tools-galaxyp/> +- Galaxy Tool Shed: <http://toolshed.g2.bx.psu.edu/view/galaxyp/peptideshaker> +- Tool ID: `peptideshaker`, `search_gui` + + +Description +----------- + +Perform protein identification combining numerous search engines (using SearchGUI) followed by peptide and protein inference with PeptideShaker. + +Includes tool wrappers for SearchGUI and PeptideShaker. The SearchGUI tool takes any number of mgf files and performs searches on these. It creates a large zip archive with all search results, the original database and spectra. This can then be fed to the PeptideShaker tool which merges the results and performs peptide and protein inference. + + +Configuration +------------- + +This tool requires a Java runtime 1.6 or greater to work. To avoid out of memory errors you should set the maximum heapspace for java processes as the default is most likely too small. For example, to set this in your shell: + + export _JAVA_OPTIONS='-Xmx1500M' + +On some systems you may also need to adjust the amount of memory available for class definitions in addition to the maximum heapspace. For example: + + export _JAVA_OPTIONS='-Xmx1500M -XX:MaxPermSize=256M' + +It is also possible to set this on a per tool basis using advanced features of the galaxy job config system. + +Note: + +- 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_ and other information can be found at: + +<https://github.com/galaxyproteomics> + +.. _GalaxyP: https://github.com/galaxyproteomics/ + + +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://github.com/galaxyproteomics/tools-galaxyp/> + + +Authors +------- + +Authors and contributors: + +* Bjoern Gruening <bjoern.gruening@gmail.com> +* Ira Cooke +* Cody Wang +* Fred Sadler +* John Chilton <jmchilton@gmail.com> +* Minnesota Supercomputing Institute, Univeristy of Minnesota
--- a/peptide_shaker.xml Tue Mar 24 19:58:38 2015 -0400 +++ b/peptide_shaker.xml Mon May 04 20:25:30 2015 -0400 @@ -1,9 +1,9 @@ -<tool id="peptide_shaker" name="Peptide Shaker" version="0.37.0"> +<tool id="peptide_shaker" name="Peptide Shaker" version="0.38.0"> <description> Perform protein identification using various search engines based on results from SearchGUI </description> <requirements> - <requirement type="package" version="0.37">peptide_shaker</requirement> + <requirement type="package" version="0.38">peptide_shaker</requirement> </requirements> <macros> <import>macros.xml</import> @@ -474,7 +474,7 @@ <param name="filtering_options_selector" type="select" label="Specify Advanced Filtering Options" help="Filter based on peptide lengths, precursor mass error, E value errors from X! Tandem and OMSSA, and include/exclude unknown PTM’s"> <option value="no" selected="True">Default Filtering Options</option> - <option value="yes">Advanced Processing Options</option> + <option value="yes">Advanced Filtering Options</option> </param> <when value="no" /> <when value="yes">
--- a/searchgui.xml Tue Mar 24 19:58:38 2015 -0400 +++ b/searchgui.xml Mon May 04 20:25:30 2015 -0400 @@ -1,9 +1,9 @@ -<tool id="search_gui" name="Search GUI" version="1.26.0"> +<tool id="search_gui" name="Search GUI" version="1.27.0"> <description> Perform protein identification using various search engines and prepare results for input to Peptide Shaker </description> <requirements> - <requirement type="package" version="1.26">searchgui</requirement> + <requirement type="package" version="1.27">searchgui</requirement> </requirements> <macros> <import>macros.xml</import> @@ -76,7 +76,6 @@ #end if #if $advanced.msgf.msgf_selector == "yes" - -msgf_decoy ${advanced.msgf.msgf_decoy} -msgf_min_pep_length ${advanced.msgf.msgf_min_pep_length} -msgf_max_pep_length ${advanced.msgf.msgf_max_pep_length} -msgf_termini ${advanced.msgf.msgf_termini} @@ -132,12 +131,6 @@ -msgf 0 #end if - #if $advanced.ms_amanda.ms_amanda_selector == "yes" - -ms_amanda 1 - #else - -ms_amanda 0 - #end if - #if $advanced.myrimatch.myrimatch_selector == "yes" -myrimatch 1 #else @@ -150,6 +143,12 @@ -comet 0 #end if + #if $advanced.ms_amanda.ms_amanda_selector == "yes" + -ms_amanda 1 + #else + -ms_amanda 0 + #end if + #if $advanced.tide.tide_selector == "yes" -tide 1 #else @@ -157,7 +156,7 @@ #end if #else - -ms_amanda 0 + -ms_amanda 0 -tide 0 #end if ## single zip file @@ -276,8 +275,6 @@ </param> <when value="no" /> <when value="yes"> - <param name="msgf_decoy" type="boolean" truevalue="1" falsevalue="0" - label="Search Decoys" help="If yes then a decoy database will be generated and searched. Assumed input database contains no decoys"/> <param name="msgf_min_pep_length" type="integer" value="6" label="Minimum Peptide Length" help="Minimum length for a peptide to be considered"/> <param name="msgf_max_pep_length" type="integer" value="30" @@ -292,20 +289,10 @@ </when> </conditional> - <conditional name="ms_amanda"> - <param name="ms_amanda_selector" type="select" label="Run MS Amanda search"> - <option value="yes">Search with MS Amanda</option> - <option value="no" selected="True">No MS Amanda search</option> - </param> - <when value="no" /> - <when value="yes"> - </when> - </conditional> - <conditional name="myrimatch"> <param name="myrimatch_selector" type="select" label="Run MyriMatch search"> - <option value="yes">Search with MyriMatch</option> - <option value="no" selected="True">No MyriMatch search</option> + <option value="yes" selected="True">Search with MyriMatch</option> + <option value="no">No MyriMatch search</option> </param> <when value="no" /> <when value="yes"> @@ -314,8 +301,18 @@ <conditional name="comet"> <param name="comet_selector" type="select" label="Run Comet search"> - <option value="yes">Search with Comet</option> - <option value="no" selected="True">No Comet search</option> + <option value="yes" selected="True">Search with Comet</option> + <option value="no">No Comet search</option> + </param> + <when value="no" /> + <when value="yes"> + </when> + </conditional> + + <conditional name="ms_amanda"> + <param name="ms_amanda_selector" type="select" label="Run MS Amanda search"> + <option value="yes">Search with MS Amanda</option> + <option value="no" selected="True">No MS Amanda search</option> </param> <when value="no" /> <when value="yes"> @@ -359,8 +356,9 @@ <help> **What it does** -Runs multiple search engines (X! Tandem, OMSSA and MS-GF+) on any number of MGF peak lists using the SearchGUI. +Runs multiple search engines on any number of MGF peak lists using the SearchGUI. +By default X! Tandem, OMSSA, MS-GF+, Myrimatch and Comet are run. Optionally, Amanda and Tide engines can also be run. </help> <expand macro="citations" />
--- a/tool_dependencies.xml Tue Mar 24 19:58:38 2015 -0400 +++ b/tool_dependencies.xml Mon May 04 20:25:30 2015 -0400 @@ -1,9 +1,9 @@ <?xml version="1.0"?> <tool_dependency> - <package name="searchgui" version="1.26"> - <repository changeset_revision="fb933e6821a5" name="package_searchgui_1_26" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + <package name="searchgui" version="1.27"> + <repository changeset_revision="6f6961d6bea5" name="package_searchgui_1_27" owner="iracooke" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> - <package name="peptide_shaker" version="0.37"> - <repository changeset_revision="66083145a3b8" name="package_peptideshaker_0_37" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + <package name="peptide_shaker" version="0.38"> + <repository changeset_revision="3b8f4f9f93d2" name="package_peptideshaker_0_38" owner="iracooke" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> </tool_dependency>