Mercurial > repos > bornea > saint_preprocessing
comparison SAINT_preprocessing.xml @ 63:1972ccdbeb16 draft
Uploaded
author | bornea |
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date | Sat, 27 Aug 2016 22:12:01 -0400 |
parents | 81db20bfc349 |
children | e382e24af909 |
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62:81db20bfc349 | 63:1972ccdbeb16 |
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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 $Inter_file $Prey_file | 33 \$INSTALL_RUN_PATH/ $type_select.bait_bool $type_select.bait_file_in $Inter_file $Prey_file |
34 #elif (str($type_select.type) == 'mzIdentML'): | |
35 Protein_report_processing.py "$type_select.input" $type_select.bait_file_in $type_select.preybool $type_select.fasta_db \$INSTALL_RUN_PATH/ | |
36 " | |
37 #for $ba in $bait | |
38 ${ba.bait1} | |
39 ${ba.assign} | |
40 ${ba.T_C} | |
41 #end for | |
42 " | |
43 $type_select.bait_bool $Prey_file $Bait_file $Inter_file | |
34 #end if | 44 #end if |
35 </command> | 45 </command> |
36 <requirements> | 46 <requirements> |
37 <requirement type="set_environment">INSTALL_RUN_PATH</requirement> | 47 <requirement type="set_environment">INSTALL_RUN_PATH</requirement> |
38 </requirements> | 48 </requirements> |
40 <conditional name="type_select"> | 50 <conditional name="type_select"> |
41 <param type="select" name="type" label="Data Source"> | 51 <param type="select" name="type" label="Data Source"> |
42 <option value="MaxQuant">MaxQuant</option> | 52 <option value="MaxQuant">MaxQuant</option> |
43 <option value="Scaffold">Scaffold</option> | 53 <option value="Scaffold">Scaffold</option> |
44 <option value="Peptideshaker">Peptideshaker</option> | 54 <option value="Peptideshaker">Peptideshaker</option> |
55 <option value="mzIdentML">mzIdentML</option> | |
45 </param> | 56 </param> |
46 <when value="MaxQuant"> | 57 <when value="MaxQuant"> |
47 <param format="dat" name="input" type="data" label="MaxQuant peptides Output"/> | 58 <param format="dat" name="input" type="data" label="MaxQuant peptides Output"/> |
48 <param type="boolean" name="preybool" checked="true" label="Create Prey File"/> | 59 <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"/> | 60 <param type="data" name="fasta_db" format="fasta" label="Provide Uniprot Fasta database" optional="true"/> |
64 <option value="Peptides">#Peptides</option> | 75 <option value="Peptides">#Peptides</option> |
65 <option value="Unique">#Unique</option> | 76 <option value="Unique">#Unique</option> |
66 <option value="Validated_PSMs">#Validated PSMs</option> | 77 <option value="Validated_PSMs">#Validated PSMs</option> |
67 <option value="PSMs">#PSMs</option> | 78 <option value="PSMs">#PSMs</option> |
68 </param> | 79 </param> |
80 <param type="boolean" name="preybool" checked="true" label="Create Prey File"/> | |
81 <param type="data" name="fasta_db" format="fasta" label="Provide Uniprot Fasta database" optional="true"/> | |
82 <param name="bait_bool" type="boolean" checked="true" label="Are You Providing Your Own bait file?"/> | |
83 <param type="data" format="dat" name="bait_file_in" label="Bait File" optional="true"/> | |
84 </when> | |
85 <when value="mzIdentML"> | |
86 <param format="dat" name="input" type="data" label="mzIdentML Files" multiple="true"/> | |
69 <param type="boolean" name="preybool" checked="true" label="Create Prey File"/> | 87 <param type="boolean" name="preybool" checked="true" label="Create Prey File"/> |
70 <param type="data" name="fasta_db" format="fasta" label="Provide Uniprot Fasta database" optional="true"/> | 88 <param type="data" name="fasta_db" format="fasta" label="Provide Uniprot Fasta database" optional="true"/> |
71 <param name="bait_bool" type="boolean" checked="true" label="Are You Providing Your Own bait file?"/> | 89 <param name="bait_bool" type="boolean" checked="true" label="Are You Providing Your Own bait file?"/> |
72 <param type="data" format="dat" name="bait_file_in" label="Bait File" optional="true"/> | 90 <param type="data" format="dat" name="bait_file_in" label="Bait File" optional="true"/> |
73 </when> | 91 </when> |