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comparison peptide_shaker.xml @ 12:d298e0b6fd72 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 464dc333f2e8d359265e1574b01386c4e7e9d840
author iracooke
date Tue, 11 Aug 2015 15:55:30 -0400
parents 9d12b1d3c4ef
children 3ccfbb673089
comparison
equal deleted inserted replaced
11:76d14dc397ed 12:d298e0b6fd72
14 #from datetime import datetime 14 #from datetime import datetime
15 #set $exp_str = "Galaxy_Experiment_%s" % datetime.now().strftime("%Y%m%d%H%M%s") 15 #set $exp_str = "Galaxy_Experiment_%s" % datetime.now().strftime("%Y%m%d%H%M%s")
16 #set $samp_str = "Sample_%s" % datetime.now().strftime("%Y%m%d%H%M%s") 16 #set $samp_str = "Sample_%s" % datetime.now().strftime("%Y%m%d%H%M%s")
17 #set $temp_stderr = "peptideshaker_stderr" 17 #set $temp_stderr = "peptideshaker_stderr"
18 18
19
19 mkdir output_reports; 20 mkdir output_reports;
20 cwd=`pwd`; 21 cwd=`pwd`;
22
23 cp -r "\${PEPTIDESHAKER_JAR_PATH%/*}" bin;
24 tmp_peptideshaker_jar_path=`echo "\$cwd/bin/\${PEPTIDESHAKER_JAR_PATH\#\#/*/}"`;
21 25
22 ln -s '$searchgui_input' searchgui_input.zip && 26 ln -s '$searchgui_input' searchgui_input.zip &&
23 ###################### 27 ######################
24 ## PeptideShakerCLI ## 28 ## PeptideShakerCLI ##
25 ###################### 29 ######################
26 (java -cp \$PEPTIDESHAKER_JAR_PATH eu.isas.peptideshaker.cmd.PeptideShakerCLI 30 (java -cp \$tmp_peptideshaker_jar_path eu.isas.peptideshaker.cmd.PeptideShakerCLI
27 -temp_folder \$cwd/PeptideShakerCLI 31 -temp_folder \$cwd/PeptideShakerCLI
28 -experiment '$exp_str' 32 -experiment '$exp_str'
29 -sample '$samp_str' 33 -sample '$samp_str'
30 -replicate 1 34 -replicate 1
31 -identification_files \$cwd/searchgui_input.zip 35 -identification_files \$cwd/searchgui_input.zip
78 ## PeptideShaker Report options ## 82 ## PeptideShaker Report options ##
79 ################################## 83 ##################################
80 84
81 #if 'mzidentML' in str($outputs).split(','): 85 #if 'mzidentML' in str($outputs).split(','):
82 echo "Generating mzIdentML"; 86 echo "Generating mzIdentML";
83 (java -cp \$PEPTIDESHAKER_JAR_PATH eu.isas.peptideshaker.cmd.MzidCLI 87 (java -cp \$tmp_peptideshaker_jar_path eu.isas.peptideshaker.cmd.MzidCLI
84 -in \$cwd/peptideshaker_output.zip 88 -in \$cwd/peptideshaker_output.zip
85 -output_file output.mzid 89 -output_file output.mzid
86 -contact_first_name "Proteomics" 90 -contact_first_name "Proteomics"
87 -contact_last_name "Galaxy" 91 -contact_last_name "Galaxy"
88 -contact_email "galaxyp@umn.edu" 92 -contact_email "galaxyp@umn.edu"
97 ## Generate Reports if the user has selected one of the 8 additional reports 101 ## Generate Reports if the user has selected one of the 8 additional reports
98 ## 'cps', 'mzidentML' and 'zip' are not valid options for PeptideShaker 102 ## 'cps', 'mzidentML' and 'zip' are not valid options for PeptideShaker
99 ## and will not be passed to the command line 103 ## and will not be passed to the command line
100 #if set(["0","1","2","3","4","5","6","7"]).intersection( set( str( $outputs ).split(',') ) ): 104 #if set(["0","1","2","3","4","5","6","7"]).intersection( set( str( $outputs ).split(',') ) ):
101 105
102 (java -cp \$PEPTIDESHAKER_JAR_PATH eu.isas.peptideshaker.cmd.ReportCLI 106 (java -cp \$tmp_peptideshaker_jar_path eu.isas.peptideshaker.cmd.ReportCLI
103 -temp_folder \$cwd/ReportCLI 107 -temp_folder \$cwd/ReportCLI
104 -in \$cwd/peptideshaker_output.zip 108 -in \$cwd/peptideshaker_output.zip
105 -out_reports \$cwd/output_reports 109 -out_reports \$cwd/output_reports
106 #set $cleaned_list = str($outputs).split(',') 110 #set $cleaned_list = str($outputs).split(',')
107 #if 'cps' in $cleaned_list: 111 #if 'cps' in $cleaned_list: