Mercurial > repos > bgruening > peptideshaker
changeset 19:05f020f19ef6 draft
Uploaded
| author | iracooke |
|---|---|
| date | Tue, 24 Jun 2014 17:09:06 -0400 |
| parents | 22babad2d8f2 |
| children | 776501ce66d8 |
| files | peptide_shaker.xml |
| diffstat | 1 files changed, 15 insertions(+), 10 deletions(-) [+] |
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--- a/peptide_shaker.xml Fri Jun 20 15:42:17 2014 -0400 +++ b/peptide_shaker.xml Tue Jun 24 17:09:06 2014 -0400 @@ -1,15 +1,16 @@ -<tool id="peptide_shaker" name="Peptide Shaker" version="1.19.4.0"> +<tool id="peptide_shaker" name="Peptide Shaker" version="1.19.5.0"> <description> Perform protein identification using various search engines (using SearchGUI) and combine results with PeptideShaker. </description> <requirements> - <requirement type="package" version="0.31.3">peptide_shaker</requirement> - <requirement type="package" version="1.19.4">searchgui</requirement> + <requirement type="package" version="0.31.4">peptide_shaker</requirement> + <requirement type="package" version="1.19.5">searchgui</requirement> <!--<requirement type="package" version="2.2.29">blast+</requirement>--> </requirements> <stdio> <exit_code range="1:" level="fatal" description="Job Failed" /> - <regex match="Error" level="fatal" description="Error encounterd!"/> + <regex match="java.*Exception" level="fatal" description="Java Exception"/> + <regex match="Could not create the Java virtual machine" level="fatal" description="JVM Error"/> </stdio> <command> @@ -154,7 +155,10 @@ -ms_amanda 0 #end if + #else + -ms_amanda 0 #end if + 2>> $temp_stderr) && @@ -241,13 +245,14 @@ -temp_folder `pwd` -in \$cwd/peptide_shaker_output.cps -out_reports \$cwd/output_reports - #if 'cps' in str($outputs).split(','): - #set $cleaned_list = str($outputs).split(',') + #set $cleaned_list = str($outputs).split(',') + #if 'cps' in $cleaned_list: #silent $cleaned_list.remove('cps') - -reports #echo ','.join($cleaned_list)# - #else: - -reports #echo str($outputs)# #end if + #if 'mzidentML' in $cleaned_list: + #silent $cleaned_list.remove('mzidentML') + #end if + -reports #echo ','.join($cleaned_list)# 2>> $temp_stderr) && @@ -793,7 +798,7 @@ <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. +Runs multiple search engines (X! Tandem, OMSSA and MS-GF+) on any number of MGF peak lists using the SearchGUI application and combines the results. https://code.google.com/p/peptide-shaker/