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comparison SAINT_preprocessing.xml @ 60:3c0ed536029e draft

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author bornea
date Sat, 27 Aug 2016 21:29:26 -0400
parents 5ad68d3a11cc
children 0b4450bdc6a9
comparison
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59:5ad68d3a11cc 60:3c0ed536029e
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($type) == 'Scaffold'): 4 #if (str($type_select.type) == 'Scaffold'):
5 SAINT_preprocessing.py $input $preybool $fasta_db $Inter_file $Prey_file 5 SAINT_preprocessing.py $input $preybool $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 $Bait_file \$INSTALL_RUN_PATH/ $bait_bool $bait_file_in 13 $Bait_file \$INSTALL_RUN_PATH/ $bait_bool $bait_file_in
14 #elif (str($type) == 'MaxQuant'): 14 #elif (str($type_select.type) == 'MaxQuant'):
15 SAINT_preprocessing_mq_pep.py $input $preybool $fasta_db $Inter_file $Prey_file 15 SAINT_preprocessing_mq_pep.py $input $preybool $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 $Bait_file \$INSTALL_RUN_PATH/ $bait_bool $bait_file_in 23 $Bait_file \$INSTALL_RUN_PATH/ $bait_bool $bait_file_in
24 #elif (str($type) == 'Peptideshaker'): 24 #elif (str($type_select.type) == 'Peptideshaker'):
25 Protein_report_processing.py "$input" $Bait_file $use_metric $fasta_db $preybool 25 Protein_report_processing.py "$input" $Bait_file $use_metric $fasta_db $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}
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>
39 <inputs> 39 <inputs>
40 <conditional name="type_select"> 40 <conditional name="type_select">
41 <param type="select" name="type" label="MaxQuant or Scaffold"> 41 <param type="select" name="type" label="Data Source">
42 <option value="MaxQuant">MaxQuant</option> 42 <option value="MaxQuant">MaxQuant</option>
43 <option value="Scaffold">Scaffold</option> 43 <option value="Scaffold">Scaffold</option>
44 <option value="Peptideshaker">Peptideshaker</option> 44 <option value="Peptideshaker">Peptideshaker</option>
45 </param> 45 </param>
46 <when value="MaxQuant"> 46 <when value="MaxQuant">