Mercurial > repos > jjohnson > msfragger

comparison msfragger.xml @ 1:a2e41fca9e39 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author jjohnson
date Tue, 29 Aug 2017 15:57:14 -0400
parents 9cbe178a3e3c
children
comparison
equal deleted inserted replaced
0:9cbe178a3e3c 1:a2e41fca9e39
8 cat $fragger_params > '$param_file' 8 cat $fragger_params > '$param_file'
9 ## 9 ##
10 && echo " " >> '$param_file' 10 && echo " " >> '$param_file'
11 && echo "num_threads = \$GALAXY_SLOTS" >> '$param_file' 11 && echo "num_threads = \$GALAXY_SLOTS" >> '$param_file'
12 && cat $param_file > '$output_params' 12 && cat $param_file > '$output_params'
13 && cat /Users/jj/gxt/gxt/database/files/009/dataset_9448.dat > Uniprot.20151009.Hs.revDecoys.fa
14 #if $input.extension == 'mzml': 13 #if $input.extension == 'mzml':
15 #set $file_ext = 'mzML' 14 #set $file_ext = 'mzML'
16 #elif $input.extension == 'mzxml': 15 #elif $input.extension == 'mzxml':
17 #set $file_ext = 'mzXML' 16 #set $file_ext = 'mzXML'
18 #elif $input.extension == 'mgf': 17 #elif $input.extension == 'mgf':
22 #set $input_path = $input_prefix.__str__ + "_rep" + str($i + 1) + "." + $file_ext 21 #set $input_path = $input_prefix.__str__ + "_rep" + str($i + 1) + "." + $file_ext
23 #else: 22 #else:
24 #set $input_path = $re.sub('\.[mM]\w+$','',$re.sub('[^-a-zA-Z0-9_.]','_',$input.name)) + "." + $file_ext 23 #set $input_path = $re.sub('\.[mM]\w+$','',$re.sub('[^-a-zA-Z0-9_.]','_',$input.name)) + "." + $file_ext
25 #end if 24 #end if
26 && ln -s '${input}' '$input_path' 25 && ln -s '${input}' '$input_path'
27 && java -Xmx8G -jar $__tool_directory__/MSFragger.jar fragger.params '$input_path' 26 && java -Xmx30G -jar $__tool_directory__/MSFragger.jar fragger.params '$input_path'
28 ## && cat *.log 27 ## && cat *.log
29 >> "$logfile" 28 >> "$logfile"
30 #if $output_format == 'pepXML': 29 #if $output_format == 'pepXML':
31 && cat *.pep.xml > $output_pepxml 30 && cat *.pep.xml > $output_pepxml
32 #else 31 #else
118 output_file_extension = #if $output_format == 'pepXML' then 'pep.xml' else 'tsv'# ##pepXML 117 output_file_extension = #if $output_format == 'pepXML' then 'pep.xml' else 'tsv'# ##pepXML
119 output_format = $output_format ##pepXML or tsv 118 output_format = $output_format ##pepXML or tsv
120 119
121 ## additional modifications 120 ## additional modifications
122 static_modification 121 static_modification
123 s/^\(add_[^ ]*\) = \([0-9.]*\)/\1 = #if str( $static_modification.\1 ) then $static_modification.\1 else \2#/
124 122
125 add_Cterm_peptide = #if str( $static_modification.add_Cterm_peptide ) then $static_modification.add_Cterm_peptide else 0.0# 123 add_Cterm_peptide = #if str( $static_modification.add_Cterm_peptide ) then $static_modification.add_Cterm_peptide else 0.0#
126 add_Nterm_peptide = #if str( $static_modification.add_Nterm_peptide ) then $static_modification.add_Nterm_peptide else 0.0# 124 add_Nterm_peptide = #if str( $static_modification.add_Nterm_peptide ) then $static_modification.add_Nterm_peptide else 0.0#
127 add_Cterm_protein = #if str( $static_modification.add_Cterm_protein ) then $static_modification.add_Cterm_protein else 0.0# 125 add_Cterm_protein = #if str( $static_modification.add_Cterm_protein ) then $static_modification.add_Cterm_protein else 0.0#
128 add_Nterm_protein = #if str( $static_modification.add_Nterm_protein ) then $static_modification.add_Nterm_protein else 0.0# 126 add_Nterm_protein = #if str( $static_modification.add_Nterm_protein ) then $static_modification.add_Nterm_protein else 0.0#
583 - selenocysteine : 47.944449 581 - selenocysteine : 47.944449
584 - carboxymethylated selenocysteine : 105.949928 582 - carboxymethylated selenocysteine : 105.949928
585 583
586 ]]> 584 ]]>
587 </help> 585 </help>
586 <citations>
587 <citation type="doi">doi:10.1038/nmeth.4256</citation>
588 </citations>
588 </tool> 589 </tool>