Mercurial > repos > galaxyp > peptideshaker
changeset 13:3ccfbb673089 draft
Update to PS 1.1 and SG 2.1.1
author | iracooke |
---|---|
date | Thu, 15 Oct 2015 16:19:59 -0400 |
parents | d298e0b6fd72 |
children | 0c50fe88ebfc |
files | macros.xml peptide_shaker.xml searchgui.xml |
diffstat | 3 files changed, 20 insertions(+), 6 deletions(-) [+] |
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--- a/macros.xml Tue Aug 11 15:55:30 2015 -0400 +++ b/macros.xml Thu Oct 15 16:19:59 2015 -0400 @@ -25,7 +25,8 @@ -fi $forward_ion -ri $reverse_ion </token> - + <token name="@SEARCHGUI_MAJOR_VERSION@">2</token> + <token name="@SEARCH_GUI_VERION@">2.1</token> <xml name="general_options"> <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">
--- a/peptide_shaker.xml Tue Aug 11 15:55:30 2015 -0400 +++ b/peptide_shaker.xml Thu Oct 15 16:19:59 2015 -0400 @@ -1,4 +1,4 @@ -<tool id="peptide_shaker" name="Peptide Shaker" version="0.40.0"> +<tool id="peptide_shaker" name="Peptide Shaker" version="1.1.1"> <description> Perform protein identification using various search engines based on results from SearchGUI </description> @@ -6,7 +6,7 @@ <import>macros.xml</import> </macros> <requirements> - <requirement type="package" version="0.40">peptide_shaker</requirement> + <requirement type="package" version="1.1">peptide_shaker</requirement> </requirements> <expand macro="stdio" /> <command> @@ -166,7 +166,12 @@ </command> <inputs> <param name="searchgui_input" format="searchgui_archive" type="data" label="Compressed SearchGUI results" - help="SearchGUI Results from History"/> + help="SearchGUI Results from History"> + <options options_filter_attribute="metadata.searchgui_major_version" > + <filter type="add_value" value="@SEARCHGUI_MAJOR_VERSION@" /> + </options> + <validator type="expression" message="This version of PeptideShaker will only work with SearchGUI version: @SEARCHGUI_MAJOR_VERSION@ .">value is not None and value.metadata.searchgui_major_version == "@SEARCHGUI_MAJOR_VERSION@"</validator> + </param> <conditional name="species_type"> <param name="species_type_selector" type="select" optional="true" label="The species type to use for the gene annotation" @@ -178,6 +183,7 @@ <option value="Protists">Protists</option> <option value="no_species_type" selected="true">No species restriction</option> </param> + <when value="no_species_type"/> <when value="Protists"> <param name="species" type="select" label="The species to use for the gene annotation" help="">
--- a/searchgui.xml Tue Aug 11 15:55:30 2015 -0400 +++ b/searchgui.xml Thu Oct 15 16:19:59 2015 -0400 @@ -1,4 +1,4 @@ -<tool id="search_gui" name="Search GUI" version="1.28.0"> +<tool id="search_gui" name="Search GUI" version="2.1.1"> <description> Perform protein identification using various search engines and prepare results for input to Peptide Shaker </description> @@ -6,7 +6,7 @@ <import>macros.xml</import> </macros> <requirements> - <requirement type="package" version="1.28">searchgui</requirement> + <requirement type="package" version="2.1">searchgui</requirement> <environment_variable name="LC_ALL" action="set_to">C</environment_variable> </requirements> <expand macro="stdio" /> @@ -22,6 +22,9 @@ cwd=`pwd`; export HOME=\$cwd; + # Create a searchgui.properties file for the version, which will be added to the searchgui_results if not already present + echo "searchgui.version=@SEARCHGUI_VERSION@" >> searchgui.properties; + cp -r "\${SEARCHGUI_JAR_PATH%/*}" bin; tmp_searchgui_jar_path=`echo "\$cwd/bin/\${SEARCHGUI_JAR_PATH\#\#/*/}"`; @@ -330,6 +333,10 @@ && + (zip -u searchgui_out.zip searchgui.properties 2>> $temp_stderr) + + && + exit_code_for_galaxy=\$?; cat $temp_stderr 2>&1; (exit \$exit_code_for_galaxy)