Mercurial > repos > iracooke > msgfplus
diff msgfplus_search.xml @ 16:66a149ef79f7 draft
planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/msgfplus/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
author | iracooke |
---|---|
date | Tue, 20 Oct 2015 20:01:47 -0400 |
parents | 6c751c59ce18 |
children | 7990ee72821b |
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--- a/msgfplus_search.xml Thu Mar 26 20:04:30 2015 -0400 +++ b/msgfplus_search.xml Tue Oct 20 20:01:47 2015 -0400 @@ -1,8 +1,8 @@ <tool id="proteomics_search_msgfplus_1" name="MSGF+ MSMS Search" version="1.1.0"> <description>Run an MSGF+ Search</description> <requirements> - <container type="docker">iracooke/protk-1.4.1</container> - <requirement type="package" version="1.4">protk</requirement> + <container type="docker">iracooke/protk-1.4.3</container> + <requirement type="package" version="1.4.3">protk</requirement> <requirement type="package" version="20140210">msgfplus</requirement> <requirement type="package" version="3_0_4388">proteowizard</requirement> </requirements> @@ -47,8 +47,7 @@ --num-reported-matches=$num_reported_matches --java-mem=$java_mem - --threads $threads - + --threads "\${GALAXY_SLOTS:-12}" #if $pepxml_output_use: --pepxml #end if @@ -75,7 +74,7 @@ </conditional> <param name="input_file" type="data" format="mzml" multiple="false" label="MSMS File" help="An mzML file with MS/MS data"/> <param name="variable_mods" format="text" type="select" multiple="true" label="Variable Modifications" help="Multiple Selection Allowed"> - <options from_file="msgfplus_mods.loc"> + <options from_file="msgfplus_mods_var.loc"> <column name="name" index="0" /> <column name="value" index="2" /> </options> @@ -85,7 +84,7 @@ <param name="custom_mod" type="text" /> </repeat> <param name="fixed_mods" format="text" type="select" multiple="true" label="Fixed Modifications" help="Multiple Selection Allowed"> - <options from_file="msgfplus_mods.loc"> + <options from_file="msgfplus_mods_fix.loc"> <column name="name" index="0" /> <column name="value" index="2" /> </options> @@ -155,7 +154,6 @@ <param name="max_pep_charge" help="" type="integer" value="3" label="Maximum Peptide Charge"/> <param name="num_reported_matches" help="Number of matches per spectrum to be reported" type="integer" value="1" label="Num reported matches"/> <param name="java_mem" help="Increase this value if you get out of memory errors" type="text" size="80" value="3500M" label="Java Memory Limit"/> - <param name="threads" type="integer" value="1" label="Threads" help="Number of threads to use for search."/> <param name="pepxml_output_use" checked="true" type="boolean" label="Convert results to pepXML" help="" truevalue="true" falsevalue="false" /> </inputs> <outputs>