Mercurial > repos > jjohnson > msfragger
changeset 1:a2e41fca9e39 draft default tip
Uploaded
| author | jjohnson |
|---|---|
| date | Tue, 29 Aug 2017 15:57:14 -0400 |
| parents | 9cbe178a3e3c |
| children | |
| files | msfragger.xml |
| diffstat | 1 files changed, 4 insertions(+), 3 deletions(-) [+] |
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--- a/msfragger.xml Tue Aug 29 14:30:36 2017 -0400 +++ b/msfragger.xml Tue Aug 29 15:57:14 2017 -0400 @@ -10,7 +10,6 @@ && echo " " >> '$param_file' && echo "num_threads = \$GALAXY_SLOTS" >> '$param_file' && cat $param_file > '$output_params' -&& cat /Users/jj/gxt/gxt/database/files/009/dataset_9448.dat > Uniprot.20151009.Hs.revDecoys.fa #if $input.extension == 'mzml': #set $file_ext = 'mzML' #elif $input.extension == 'mzxml': @@ -24,7 +23,7 @@ #set $input_path = $re.sub('\.[mM]\w+$','',$re.sub('[^-a-zA-Z0-9_.]','_',$input.name)) + "." + $file_ext #end if && ln -s '${input}' '$input_path' -&& java -Xmx8G -jar $__tool_directory__/MSFragger.jar fragger.params '$input_path' +&& java -Xmx30G -jar $__tool_directory__/MSFragger.jar fragger.params '$input_path' ## && cat *.log >> "$logfile" #if $output_format == 'pepXML': @@ -120,7 +119,6 @@ ## additional modifications static_modification -s/^\(add_[^ ]*\) = \([0-9.]*\)/\1 = #if str( $static_modification.\1 ) then $static_modification.\1 else \2#/ add_Cterm_peptide = #if str( $static_modification.add_Cterm_peptide ) then $static_modification.add_Cterm_peptide else 0.0# add_Nterm_peptide = #if str( $static_modification.add_Nterm_peptide ) then $static_modification.add_Nterm_peptide else 0.0# @@ -585,4 +583,7 @@ ]]> </help> + <citations> + <citation type="doi">doi:10.1038/nmeth.4256</citation> + </citations> </tool>