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comparison proteinpilot.xml @ 0:7dcb26ce559c

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author galaxyp
date Wed, 19 Dec 2012 00:22:55 -0500
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1 <tool id="proteinpilot" version="0.2.1" name="ProteinPilot">
2 <description></description>
3 <!-- ESCAPE input and database name -->
4 <command interpreter="python">proteinpilot_wrapper.py
5 #for $input in $inputs:
6 --input="${input}"
7 --input_name="${input.name}"
8 #end for
9 --database="${database}"
10 --database_name="${database.name}"
11 --output=$output
12 --output_methods=$output_methods
13 --sample_type="$sample_type"
14 --quantitative=$quantitative
15 --bias_correction=$bias_correction
16 --background_correction=$background_correction
17 --cys_alkylation="$cys_alkylation"
18 --digestion="$digestion"
19 --instrument="$instrument"
20 --search_effort=$search_effort
21 --pspep=$pspep
22 #if $pspep
23 --output_pspep_report=$output_pspep_report
24 #end if
25 --min_unused_protscore=$min_unused_protscore
26 #if $factors.factors_use
27 --special_factors="$factors.special_factors"
28 #else
29 --special_factors=""
30 #end if
31 --search_foci="$search_foci"
32 </command>
33 <inputs>
34 <param format="mgf" multiple="true" name="inputs" type="data" label="Peaklist (MGF)" help="" />
35 <param type="select" name="sample_type" label="Sample Type">
36 <option value="Identification">Identification</option>
37 <option value="iTRAQ 4plex (Peptide Labeled)">iTRAQ 4plex (Peptide Labeled)</option>
38 <option value="iTRAQ 4plex (Protein Labeled)">iTRAQ 4plex (Protein Labeled)</option>
39 <option value="iTRAQ 8plex (Peptide Labeled)">iTRAQ 8plex (Peptide Labeled)</option>
40 <option value="iTRAQ 8plex (Protein Labeled)">iTRAQ 8plex (Protein Labeled)</option>
41 <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>
43 <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>
45 <option value="SILAC (Lys+6, Arg+6)">SILAC (Lys+6, Arg+6)</option>
46 <option value="SILAC (Lys+4, Arg+10)">SILAC (Lys+4, Arg+10)</option>
47 <option value="SILAC (Lys+6, Arg+10)">SILAC (Lys+6, Arg+10)</option>
48 <option value="SILAC (Lys+8, Arg+10)">SILAC (Lys+8, Arg+10)</option>
49 <option value="SILAC (Lys+8, Arg+10, Glu+6, Asp+5)">SILAC (Lys+8, Arg+10, Glu+6, Asp+5)</option>
50 <!-- TODO: Add remaining SILAC options. -->
51 <option value="RABA +0,+6 (Peptide Labeled)">RABA +0,+6 (Peptide Labeled)</option>
52 <option value="Dimethyl +0,+4 (Peptide Labeled)">Dimethyl +0,+4 (Peptide Labeled)</option>
53 <option value="Dimethyl +0,+6 (Peptide Labeled)">Dimethyl +0,+6 (Peptide Labeled)</option>
54 <option value="Dimethyl +0,+8 (Peptide Labeled)">Dimethyl +0,+8 (Peptide Labeled)</option>
55 <option value="Dimethyl +0,+4,+8 (Peptide Labeled)">Dimethyl +0,+4,+8 (Peptide Labeled)</option>
56 <option value="Proteolytic O-18 labeling">Proteolytic O-18 labeling</option>
57 <option value="Cleavable ICAT">Cleavable ICAT</option>
58 <option value="ICPL Light, Heavy (Peptide Labeled)">ICPL Light, Heavy (Peptide Labeled)</option>
59 <option value="ICPL Light, Heavy (Protein Labeled)">ICPL Light, Heavy (Protein Labeled)</option>
60 <!-- TODO: Handle additional mTRAQ and iTRAQ options.
61 handle TMT (doesn't seem like UI lets quantatate these)
62 <UI_SAMPLE_TYPE>TMT6plex ID-only (Peptide Labeled)</UI_SAMPLE_TYPE>
63 <UI_QUANT_TYPE></UI_QUANT_TYPE>
64
65 <UI_SAMPLE_TYPE>TMT6plex ID-only (Protein Labeled)</UI_SAMPLE_TYPE>
66 <UI_QUANT_TYPE></UI_QUANT_TYPE>
67
68 <UI_SAMPLE_TYPE>TMT2plex ID-only (Peptide Labeled)</UI_SAMPLE_TYPE>
69 <UI_QUANT_TYPE></UI_QUANT_TYPE>
70
71 <UI_SAMPLE_TYPE>TMT ID-only (Peptide Labeled)</UI_SAMPLE_TYPE>
72 <UI_QUANT_TYPE></UI_QUANT_TYPE>
73 -->
74 <option value="SILAC unlabeled, N-15 labeled">SILAC unlabeled, N-15 labeled</option>
75 </param>
76 <param type="select" name="cys_alkylation" label="Cys Alkylation">
77 <option value="None">None</option>
78 <option value="Iodoacetamide">Iodoacetamide</option>
79 <option value="MMTS">MMTS</option>
80 <option value="Acrylamide">Acrylamide</option>
81 <option value="Iodoacetic acid">Iodoacetic acid</option>
82 <option value="Iodoethanol">Iodoethanol</option>
83 <option value="Vinylpyridine">Vinylpyridine</option>
84 <option value="N-Ethylmaleimide">N-Ethylmaleimide</option>
85 <option value="N-Methylmaleimide">N-Methylmaleimide</option>
86 <option value="Iodoacetyl-PEO-Biotin">Iodoacetyl-PEO-Biotin</option>
87 <option value="Iodoacetamide with Iodoacetyl-PEO-Biotin chase">Iodoacetamide with Iodoacetyl-PEO-Biotin chase</option>
88 <option value="Iodoacetamide w other Cys mods possible">Iodoacetamide w other Cys mods possible</option>
89 <option value="MMTS w other Cys mods possible">MMTS w other Cys mods possible</option>
90 <option value="Unknown">Unknown</option>
91 </param>
92 <param type="select" name="digestion" label="Digestion">
93 <option value="Trypsin">Trypsin</option>
94 <option value="Glu C">Glu C</option>
95 <option value="Chymotrypsin">Chymotrypsin</option>
96 <option value="CNBr">CNBr</option>
97 <option value="Lys C">Lys C</option>
98 <option value="Acid Cleavage">Acid Cleavage</option>
99 <option value="Arg C">Arg C</option>
100 <option value="Asp N">Asp N</option>
101 <option value="Lys N">Lys N</option>
102 <option value="Thermolysin">Thermolysin</option>
103 <option value="Trypsin + Chymotrypsin">Trypsin + Chymotrypsin</option>
104 <option value="Trypsin + Glu C">Trypsin + Glu C</option>
105 <option value="Trypsin + Asp N">Trypsin + Asp N</option>
106 <option value="Lys C + Chymotrypsin">Lys C + Chymotrypsin</option>
107 <option value="Lys C + Glu C">Lys C + Glu C</option>
108 <option value="Glu C + Asp N">Glu C + Asp N</option>
109 <option value="Trypsin using MSIPI database">Trypsin using MSIPI database</option>
110 </param>
111 <param type="select" name="instrument" label="Instrument">
112 <option value="TripleTOF 5600">TripleTOF 5600</option>
113 <option value="TripleTOF 4600">TripleTOF 4600</option>
114 <option value="5800">5800</option>
115 <option value="4800">4800</option>
116 <option value="4700">4700</option>
117 <option value="QSTAR Elite ESI">QSTAR Elite ESI</option>
118 <option value="QSTAR Elite">QSTAR Elite</option>
119 <option value="QSTAR oMALDI">QSTAR oMALDI</option>
120 <option value="6500 QTRAP ESI">6500 QTRAP ESI</option>
121 <option value="4500 QTRAP ESI">4500 QTRAP ESI</option>
122 <option value="5500 QTRAP ESI">5500 QTRAP ESI</option>
123 <option value="4000 QTRAP ESI">4000 QTRAP ESI</option>
124 <option value="QTRAP ESI">QTRAP ESI</option>
125 <option value="4000 QTRAP AP-MALDI">4000 QTRAP AP-MALDI</option>
126 <option value="3200 QTRAP AP-MALDI">3200 QTRAP AP-MALDI</option>
127 <option value="LTQ">LTQ</option>
128 <option value="Orbi/FT MS (1-3ppm), LTQ MS/MS">Orbi/FT MS (1-3ppm), LTQ MS/MS</option>
129 <option value="Orbi/FT MS (sub-ppm), LTQ MS/MS">Orbi/FT MS (sub-ppm), LTQ MS/MS</option>
130 <option value="Orbi MS, Orbi MS/MS">Orbi MS, Orbi MS/MS</option>
131 <option value="Orbi MS (sub-ppm), Orbi MS/MS">Orbi MS (sub-ppm), Orbi MS/MS</option>
132 </param>
133 <conditional name="factors">
134 <param name="factors_use" type="boolean" label="Specify Special Factors?" help="" truevalue="true" falsevalue="false" />
135 <when value="false" />
136 <when value="true">
137 <param type="select" name="special_factors" label="Special Factors" display="checkboxes" multiple="true" help="">
138 <option value="Phosphorylation emphasis">Phosphorylation emphasis</option>
139 <option value="Methyl esterification">Methyl esterification</option>
140 <option value="Phos-Tyr affinity column">Phos-Tyr affinity column</option>
141 <option value="Gel-based ID">Gel-based ID</option>
142 <option value="Urea denaturation">Urea denaturation</option>
143 <option value="Acetylation emphasis">Acetylation emphasis</option>
144 <option value="Ubiquitin/SUMO enrichment">Ubiquitin/SUMO enrichment</option>
145 <option value="BONCAT workflow">BONCAT workflow</option>
146 <option value="PNGase F in O-18 water">PNGase F in O-18 water</option>
147 <option value="Pronota">Pronota</option>
148 <option value="O-methylisourea treatment">O-methylisourea treatment</option>
149 <option value="Purified Histones">Purified Histones</option>
150 <option value="Propionylation pre-digestion">Propionylation pre-digestion</option>
151 <option value="Propionylation post-digestion">Propionylation post-digestion</option>
152 <option value="Deuteroacetylation pre-digestion">Deuteroacetylation pre-digestion</option>
153 <option value="Deuteroacetylation post-digestion">Deuteroacetylation post-digestion</option>
154 <option value="Iodo and Thyroxine mods enrichment">Iodo and Thyroxine mods enrichment</option>
155 </param>
156 </when>
157 </conditional>
158 <param format="fasta" name="database" type="data" label="Database" />
159 <param name="quantitative" type="boolean" truevalue="True" falsevalue="False" label="Run Quantitation (if applicable)" checked="False" help="" />
160 <param name="background_correction" type="boolean" truevalue="True" falsevalue="False" label="Use Background Correction (if applicable)" checked="False" help="" />
161 <param name="bias_correction" type="boolean" truevalue="True" falsevalue="False" label="Use Bias Correction (if applicable)" checked="False" help="" />
162 <param type="select" name="search_foci" label="Search Focus" display="checkboxes" multiple="true" help="">
163 <option value="Biological modifications">Biological modifications</option>
164 <option value="Amino acid substitutions">Amino acid substitutions</option>
165 </param>
166 <param name="search_effort" type="boolean" truevalue="Thorough" falsevalue="Rapid" label="Thorough Search" checked="True" help="" />
167 <param name="pspep" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Use PSPEP" checked="True" help="" />
168 <param type="select" name="min_unused_protscore" label="Detected Protein Threshold [Unused ProtScore (Conf)]">
169 <option value="3.0">3.0 (99.9)</option>
170 <option value="2.0">2.0 (99.0%)</option>
171 <option value="1.3">1.3 (95.0%)</option>
172 <option value="1.0">1.0 (90.0%)</option>
173 <option value="0.70">0.70 (80.0%)</option>
174 <option value="0.47">0.47 (66.0%)</option>
175 <option value="0.10">0.10 (20.0%)</option>
176 <option value="0.05" selected="true">0.05 (10.0%)</option>
177 </param>
178 </inputs>
179 <outputs>
180 <data format="group" name="output" label="ProteinPilot results for ${on_string}"/>
181 <data format="xml" name="output_methods" label="ProteinPilot methods xml for ${on_string}" />
182 <data format="xlsx" name="output_pspep_report" label="ProteinPilot PSPEP Report for ${on_string}">
183 <filter>pspep</filter>
184 </data>
185 </outputs>
186 <help>
187 </help>
188 </tool>