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comparison proteinpilot.xml @ 1:790d80981060

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Update.
author galaxyp
date Fri, 10 May 2013 18:04:15 -0400
parents 7dcb26ce559c
children 0aa9d080713e
comparison
equal deleted inserted replaced
0:7dcb26ce559c 1:790d80981060
1 <tool id="proteinpilot" version="0.2.1" name="ProteinPilot"> 1 <tool id="proteinpilot" version="0.2.1" name="ProteinPilot">
2 <description></description> 2 <description></description>
3 <!-- ESCAPE input and database name --> 3 <!-- ESCAPE input and database name -->
4 <configfiles>
5 <configfile name="input_config">## Describe input groups
6 group:DEFAULT_GROUP
7 #for $input in $inputs:
8 name:${input.display_name}
9 path:${input}
10 #end for
11 </configfile>
12 </configfiles>
4 <command interpreter="python">proteinpilot_wrapper.py 13 <command interpreter="python">proteinpilot_wrapper.py
5 #for $input in $inputs: 14 --input_config="$input_config"
6 --input="${input}"
7 --input_name="${input.name}"
8 #end for
9 --database="${database}" 15 --database="${database}"
10 --database_name="${database.name}" 16 --database_name="${database.display_name}"
11 --output=$output 17 --output=$output
12 --output_methods=$output_methods 18 --output_methods=$output_methods
13 --sample_type="$sample_type" 19 --sample_type="$sample_type"
14 --quantitative=$quantitative 20 --quantitative=$quantitative
15 --bias_correction=$bias_correction 21 --bias_correction=$bias_correction
36 <option value="Identification">Identification</option> 42 <option value="Identification">Identification</option>
37 <option value="iTRAQ 4plex (Peptide Labeled)">iTRAQ 4plex (Peptide Labeled)</option> 43 <option value="iTRAQ 4plex (Peptide Labeled)">iTRAQ 4plex (Peptide Labeled)</option>
38 <option value="iTRAQ 4plex (Protein Labeled)">iTRAQ 4plex (Protein Labeled)</option> 44 <option value="iTRAQ 4plex (Protein Labeled)">iTRAQ 4plex (Protein Labeled)</option>
39 <option value="iTRAQ 8plex (Peptide Labeled)">iTRAQ 8plex (Peptide Labeled)</option> 45 <option value="iTRAQ 8plex (Peptide Labeled)">iTRAQ 8plex (Peptide Labeled)</option>
40 <option value="iTRAQ 8plex (Protein Labeled)">iTRAQ 8plex (Protein Labeled)</option> 46 <option value="iTRAQ 8plex (Protein Labeled)">iTRAQ 8plex (Protein Labeled)</option>
47 <option value="TMT6plex ID-only (Peptide Labeled)">TMT6plex ID-only (Peptide Labeled)</option>
48 <option value="TMT6plex ID-only (Protein Labeled)">TMT6plex ID-only (Protein Labeled)</option>
49 <option value="TMT2plex ID-only (Peptide Labeled)">TMT2plex ID-only (Peptide Labeled)</option>
50 <option value="TMT ID-only (Peptide Labeled)">TMT ID-only (Peptide Labeled)</option>
41 <option value="mTRAQ (Peptide Labeled - M00, M04)">mTRAQ (Peptide Labeled - M00, M04)</option> 51 <option value="mTRAQ (Peptide Labeled - M00, M04)">mTRAQ (Peptide Labeled - M00, M04)</option>
42 <option value="mTRAQ (Peptide Labeled - M00, M08)">mTRAQ (Peptide Labeled - M00, M08)</option> 52 <option value="mTRAQ (Peptide Labeled - M00, M08)">mTRAQ (Peptide Labeled - M00, M08)</option>
43 <option value="mTRAQ (Peptide Labeled - M04, M08)">mTRAQ (Peptide Labeled - M04, M08)</option> 53 <option value="mTRAQ (Peptide Labeled - M04, M08)">mTRAQ (Peptide Labeled - M04, M08)</option>
44 <option value="mTRAQ (Peptide Labeled - M00, M04, M08)">mTRAQ (Peptide Labeled - M00, M04, M08)</option> 54 <option value="mTRAQ (Peptide Labeled - M00, M04, M08)">mTRAQ (Peptide Labeled - M00, M04, M08)</option>
45 <option value="SILAC (Lys+6, Arg+6)">SILAC (Lys+6, Arg+6)</option> 55 <option value="SILAC (Lys+6, Arg+6)">SILAC (Lys+6, Arg+6)</option>
60 <!-- TODO: Handle additional mTRAQ and iTRAQ options. 70 <!-- TODO: Handle additional mTRAQ and iTRAQ options.
61 handle TMT (doesn't seem like UI lets quantatate these) 71 handle TMT (doesn't seem like UI lets quantatate these)
62 <UI_SAMPLE_TYPE>TMT6plex ID-only (Peptide Labeled)</UI_SAMPLE_TYPE> 72 <UI_SAMPLE_TYPE>TMT6plex ID-only (Peptide Labeled)</UI_SAMPLE_TYPE>
63 <UI_QUANT_TYPE></UI_QUANT_TYPE> 73 <UI_QUANT_TYPE></UI_QUANT_TYPE>
64 74
65 <UI_SAMPLE_TYPE>TMT6plex ID-only (Protein Labeled)</UI_SAMPLE_TYPE> 75 <UI_SAMPLE_TYPE></UI_SAMPLE_TYPE>
66 <UI_QUANT_TYPE></UI_QUANT_TYPE> 76 <UI_QUANT_TYPE></UI_QUANT_TYPE>
67 77
68 <UI_SAMPLE_TYPE>TMT2plex ID-only (Peptide Labeled)</UI_SAMPLE_TYPE> 78 <UI_SAMPLE_TYPE>TMT2plex ID-only (Peptide Labeled)</UI_SAMPLE_TYPE>
69 <UI_QUANT_TYPE></UI_QUANT_TYPE> 79 <UI_QUANT_TYPE></UI_QUANT_TYPE>
70 80
105 <option value="Trypsin + Asp N">Trypsin + Asp N</option> 115 <option value="Trypsin + Asp N">Trypsin + Asp N</option>
106 <option value="Lys C + Chymotrypsin">Lys C + Chymotrypsin</option> 116 <option value="Lys C + Chymotrypsin">Lys C + Chymotrypsin</option>
107 <option value="Lys C + Glu C">Lys C + Glu C</option> 117 <option value="Lys C + Glu C">Lys C + Glu C</option>
108 <option value="Glu C + Asp N">Glu C + Asp N</option> 118 <option value="Glu C + Asp N">Glu C + Asp N</option>
109 <option value="Trypsin using MSIPI database">Trypsin using MSIPI database</option> 119 <option value="Trypsin using MSIPI database">Trypsin using MSIPI database</option>
120 <option value="None">None</option>
110 </param> 121 </param>
111 <param type="select" name="instrument" label="Instrument"> 122 <param type="select" name="instrument" label="Instrument">
112 <option value="TripleTOF 5600">TripleTOF 5600</option> 123 <option value="TripleTOF 5600">TripleTOF 5600</option>
113 <option value="TripleTOF 4600">TripleTOF 4600</option> 124 <option value="TripleTOF 4600">TripleTOF 4600</option>
114 <option value="5800">5800</option> 125 <option value="5800">5800</option>