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comparison SAINT_preprocessing.xml @ 61:0b4450bdc6a9 draft

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author bornea
date Sat, 27 Aug 2016 21:38:03 -0400
parents 3c0ed536029e
children 81db20bfc349
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60:3c0ed536029e 61:0b4450bdc6a9
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 $input $preybool $fasta_db $Inter_file $Prey_file 5 SAINT_preprocessing.py $type_select.input $type_select.preybool $type_select.fasta_db $type_select.Inter_file $type_select.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 $type_select.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 $input $preybool $fasta_db $Inter_file $Prey_file 15 SAINT_preprocessing_mq_pep.py $type_select.input $type_select.preybool $type_select.fasta_db $type_select.Inter_file $type_select.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 $type_select.Bait_file \$INSTALL_RUN_PATH/ $type_select.bait_bool $type_select.bait_file_in
24 #elif (str($type_select.type) == 'Peptideshaker'): 24 #elif (str($type_select.type) == 'Peptideshaker'):
25 Protein_report_processing.py "$input" $Bait_file $use_metric $fasta_db $preybool 25 Protein_report_processing.py "$type_select.input" $type_select.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/ $bait_bool $bait_file_in $Inter_file $Prey_file 33 \$INSTALL_RUN_PATH/ $type_select.bait_bool $type_select.bait_file_in $type_select.Inter_file $type_select.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>
47 <param format="dat" name="input" type="data" label="MaxQuant peptides Output"/> 47 <param format="dat" name="input" type="data" label="MaxQuant peptides Output"/>
48 <param type="boolean" name="preybool" checked="true" label="Create Prey File"/> 48 <param type="boolean" name="preybool" checked="true" label="Create Prey File"/>
49 <param type="data" name="fasta_db" format="fasta" label="Provide Uniprot Fasta database" optional="true"/> 49 <param type="data" name="fasta_db" format="fasta" label="Provide Uniprot Fasta database" optional="true"/>
50 <param name="bait_bool" type="boolean" checked="true" label="Are You Providing Your Own bait file?"/> 50 <param name="bait_bool" type="boolean" checked="true" label="Are You Providing Your Own bait file?"/>
51 <param type="data" format="dat" name="bait_file_in" label="Bait File" optional="true"/> 51 <param type="data" format="dat" name="bait_file_in" label="Bait File" optional="true"/>
52 <repeat name="bait" title="Bait Create">
53 <param name="bait1" type="text" size="100" label="Bait"/>
54 <param name="assign" type="text" size="100" label="Group Assignment"/>
55 <param name="T_C" type="boolean" checked="true" label="Is this a Control?"/>
56 </repeat>
57 </when> 52 </when>
58 <when value="Scaffold"> 53 <when value="Scaffold">
59 <param format="dat" name="input" type="data" label="Scaffold Output"/> 54 <param format="dat" name="input" type="data" label="Scaffold Output"/>
60 <param type="boolean" name="preybool" checked="true" label="Create Prey File"/> 55 <param type="boolean" name="preybool" checked="true" label="Create Prey File"/>
61 <param type="data" name="fasta_db" format="fasta" label="Provide Uniprot Fasta database" optional="true"/> 56 <param type="data" name="fasta_db" format="fasta" label="Provide Uniprot Fasta database" optional="true"/>
62 <param name="bait_bool" type="boolean" checked="true" label="Are You Providing Your Own bait file?"/> 57 <param name="bait_bool" type="boolean" checked="true" label="Are You Providing Your Own bait file?"/>
63 <param type="data" format="dat" name="bait_file_in" label="Bait File" optional="true"/> 58 <param type="data" format="dat" name="bait_file_in" label="Bait File" optional="true"/>
64 <repeat name="bait" title="Bait Create">
65 <param name="bait1" type="text" size="100" label="Bait"/>
66 <param name="assign" type="text" size="100" label="Group Assignment"/>
67 <param name="T_C" type="boolean" checked="true" label="Is this a Control?"/>
68 </repeat>
69 </when> 59 </when>
70 <when value="Peptideshaker"> 60 <when value="Peptideshaker">
71 <param format="dat" name="input" type="data" label="Peptideshaker Output" multiple="true"/> 61 <param format="dat" name="input" type="data" label="Peptideshaker Output" multiple="true"/>
72 <param type="select" name="use_metric" label="Select Report File Value for Quantification"> 62 <param type="select" name="use_metric" label="Select Report File Value for Quantification">
73 <option value="Validated_Peptides">#Validated Peptides</option> 63 <option value="Validated_Peptides">#Validated Peptides</option>
78 </param> 68 </param>
79 <param type="boolean" name="preybool" checked="true" label="Create Prey File"/> 69 <param type="boolean" name="preybool" checked="true" label="Create Prey File"/>
80 <param type="data" name="fasta_db" format="fasta" label="Provide Uniprot Fasta database" optional="true"/> 70 <param type="data" name="fasta_db" format="fasta" label="Provide Uniprot Fasta database" optional="true"/>
81 <param name="bait_bool" type="boolean" checked="true" label="Are You Providing Your Own bait file?"/> 71 <param name="bait_bool" type="boolean" checked="true" label="Are You Providing Your Own bait file?"/>
82 <param type="data" format="dat" name="bait_file_in" label="Bait File" optional="true"/> 72 <param type="data" format="dat" name="bait_file_in" label="Bait File" optional="true"/>
83 <repeat name="bait" title="Bait Create">
84 <param name="bait1" type="text" size="100" label="Bait"/>
85 <param name="assign" type="text" size="100" label="Group Assignment"/>
86 <param name="T_C" type="boolean" checked="true" label="Is this a Control?"/>
87 </repeat>
88 </when> 73 </when>
89 </conditional> 74 </conditional>
75 <repeat name="bait" title="Bait Create">
76 <param name="bait1" type="text" size="100" label="Bait"/>
77 <param name="assign" type="text" size="100" label="Group Assignment"/>
78 <param name="T_C" type="boolean" checked="true" label="Is this a Control?"/>
79 </repeat>
90 </inputs> 80 </inputs>
91 <outputs> 81 <outputs>
92 <data format="txt" name="Inter_file" label="Inter File"/> 82 <data format="txt" name="Inter_file" label="Inter File"/>
93 <data format="txt" name="Prey_file" label="Prey File" /> 83 <data format="txt" name="Prey_file" label="Prey File" />
94 <data format="txt" name="Bait_file" label="Bait File" /> 84 <data format="txt" name="Bait_file" label="Bait File" />