Mercurial > repos > bornea > saint_preprocessing

comparison SAINT_preprocessing.xml @ 62:81db20bfc349 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author bornea
date Sat, 27 Aug 2016 21:42:13 -0400
parents 0b4450bdc6a9
children 1972ccdbeb16
comparison
equal deleted inserted replaced
61:0b4450bdc6a9 62:81db20bfc349
1 <tool id="SAINT_preprocessing_v5" name="SAINT pre-processing"> 1 <tool id="SAINT_preprocessing_v5" name="SAINT pre-processing">
2 <description></description> 2 <description></description>
3 <command interpreter="python"> 3 <command interpreter="python">
4 #if (str($type_select.type) == 'Scaffold'): 4 #if (str($type_select.type) == 'Scaffold'):
5 SAINT_preprocessing.py $type_select.input $type_select.preybool $type_select.fasta_db $type_select.Inter_file $type_select.Prey_file 5 SAINT_preprocessing.py $type_select.input $type_select.preybool $type_select.fasta_db $Inter_file $Prey_file
6 " 6 "
7 #for $ba in $bait 7 #for $ba in $bait
8 ${ba.bait1} 8 ${ba.bait1}
9 ${ba.assign} 9 ${ba.assign}
10 ${ba.T_C} 10 ${ba.T_C}
11 #end for 11 #end for
12 " 12 "
13 $type_select.Bait_file \$INSTALL_RUN_PATH/ $type_select.bait_bool $type_select.bait_file_in 13 $Bait_file \$INSTALL_RUN_PATH/ $type_select.bait_bool $type_select.bait_file_in
14 #elif (str($type_select.type) == 'MaxQuant'): 14 #elif (str($type_select.type) == 'MaxQuant'):
15 SAINT_preprocessing_mq_pep.py $type_select.input $type_select.preybool $type_select.fasta_db $type_select.Inter_file $type_select.Prey_file 15 SAINT_preprocessing_mq_pep.py $type_select.input $type_select.preybool $type_select.fasta_db $Inter_file $Prey_file
16 " 16 "
17 #for $ba in $bait 17 #for $ba in $bait
18 ${ba.bait1} 18 ${ba.bait1}
19 ${ba.assign} 19 ${ba.assign}
20 ${ba.T_C} 20 ${ba.T_C}
21 #end for 21 #end for
22 " 22 "
23 $type_select.Bait_file \$INSTALL_RUN_PATH/ $type_select.bait_bool $type_select.bait_file_in 23 $Bait_file \$INSTALL_RUN_PATH/ $type_select.bait_bool $type_select.bait_file_in
24 #elif (str($type_select.type) == 'Peptideshaker'): 24 #elif (str($type_select.type) == 'Peptideshaker'):
25 Protein_report_processing.py "$type_select.input" $type_select.Bait_file $type_select.use_metric $type_select.fasta_db $type_select.preybool 25 Protein_report_processing.py "$type_select.input" $Bait_file $type_select.use_metric $type_select.fasta_db $type_select.preybool
26 " 26 "
27 #for $ba in $bait 27 #for $ba in $bait
28 ${ba.bait1} 28 ${ba.bait1}
29 ${ba.assign} 29 ${ba.assign}
30 ${ba.T_C} 30 ${ba.T_C}
31 #end for 31 #end for
32 " 32 "
33 \$INSTALL_RUN_PATH/ $type_select.bait_bool $type_select.bait_file_in $type_select.Inter_file $type_select.Prey_file 33 \$INSTALL_RUN_PATH/ $type_select.bait_bool $type_select.bait_file_in $Inter_file $Prey_file
34 #end if 34 #end if
35 </command> 35 </command>
36 <requirements> 36 <requirements>
37 <requirement type="set_environment">INSTALL_RUN_PATH</requirement> 37 <requirement type="set_environment">INSTALL_RUN_PATH</requirement>
38 </requirements> 38 </requirements>