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Update for ProteinPilot version 5.0
author Jim Johnson <jj@umn.edu>
date Thu, 05 Nov 2015 13:15:48 -0600
parents 790d80981060
children
comparison
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7:ffbfff887a03 8:0aa9d080713e
1 <tool id="proteinpilot" version="0.2.1" name="ProteinPilot"> 1 <tool id="proteinpilot" name="ProteinPilot" version="5.0.0">
2 <description></description> 2 <description></description>
3 <!-- ESCAPE input and database name --> 3 <!-- ESCAPE input and database name -->
4 <configfiles> 4 <command interpreter="python">
5 <configfile name="input_config">## Describe input groups 5 <![CDATA[
6 proteinpilot_wrapper.py
7 --input_config="$input_config"
8 --database="${database}"
9 --database_name="${database.display_name}"
10 --output=$output
11 --output_methods=$output_methods
12 --sample_type="$sample_type"
13 --quantitative=$quantitative
14 --bias_correction=$bias_correction
15 --background_correction=$background_correction
16 --cys_alkylation="$cys_alkylation"
17 --digestion="$digestion"
18 --instrument="$instrument"
19 --search_effort=$search_effort
20 --pspep=$pspep
21 #if $pspep
22 --output_pspep_report=$output_pspep_report
23 #end if
24 --min_unused_protscore=$min_unused_protscore
25 #if $factors.factors_use
26 --special_factors="$factors.special_factors"
27 #else
28 --special_factors=""
29 #end if
30 --search_foci="$search_foci"
31 ]]>
32 </command>
33 <configfiles>
34 <configfile name="input_config">## Describe input groups
6 group:DEFAULT_GROUP 35 group:DEFAULT_GROUP
7 #for $input in $inputs: 36 #for $input in $inputs:
8 name:${input.display_name} 37 name:${input.display_name}
9 path:${input} 38 path:${input}
10 #end for 39 #end for
11 </configfile> 40 </configfile>
12 </configfiles> 41 </configfiles>
13 <command interpreter="python">proteinpilot_wrapper.py 42 <inputs>
14 --input_config="$input_config" 43 <param format="mgf" multiple="true" name="inputs" type="data" label="Peaklist (MGF)" help="" />
15 --database="${database}" 44 <param type="select" name="sample_type" label="Sample Type">
16 --database_name="${database.display_name}" 45 <option value="Identification">Identification</option>
17 --output=$output 46 <option value="iTRAQ 4plex (Peptide Labeled)">iTRAQ 4plex (Peptide Labeled)</option>
18 --output_methods=$output_methods 47 <option value="iTRAQ 4plex (Protein Labeled)">iTRAQ 4plex (Protein Labeled)</option>
19 --sample_type="$sample_type" 48 <option value="iTRAQ 8plex (Peptide Labeled)">iTRAQ 8plex (Peptide Labeled)</option>
20 --quantitative=$quantitative 49 <option value="iTRAQ 8plex (Protein Labeled)">iTRAQ 8plex (Protein Labeled)</option>
21 --bias_correction=$bias_correction 50 <option value="TMT6plex ID-only (Peptide Labeled)">TMT6plex ID-only (Peptide Labeled)</option>
22 --background_correction=$background_correction 51 <option value="TMT6plex ID-only (Protein Labeled)">TMT6plex ID-only (Protein Labeled)</option>
23 --cys_alkylation="$cys_alkylation" 52 <option value="TMT2plex ID-only (Peptide Labeled)">TMT2plex ID-only (Peptide Labeled)</option>
24 --digestion="$digestion" 53 <option value="TMT ID-only (Peptide Labeled)">TMT ID-only (Peptide Labeled)</option>
25 --instrument="$instrument" 54 <option value="mTRAQ (Peptide Labeled - M00, M04)">mTRAQ (Peptide Labeled - M00, M04)</option>
26 --search_effort=$search_effort 55 <option value="mTRAQ (Peptide Labeled - M00, M08)">mTRAQ (Peptide Labeled - M00, M08)</option>
27 --pspep=$pspep 56 <option value="mTRAQ (Peptide Labeled - M04, M08)">mTRAQ (Peptide Labeled - M04, M08)</option>
28 #if $pspep 57 <option value="mTRAQ (Peptide Labeled - M00, M04, M08)">mTRAQ (Peptide Labeled - M00, M04, M08)</option>
29 --output_pspep_report=$output_pspep_report 58 <option value="SILAC (Lys+6, Arg+6)">SILAC (Lys+6, Arg+6)</option>
30 #end if 59 <option value="SILAC (Lys+4, Arg+10)">SILAC (Lys+4, Arg+10)</option>
31 --min_unused_protscore=$min_unused_protscore 60 <option value="SILAC (Lys+6, Arg+10)">SILAC (Lys+6, Arg+10)</option>
32 #if $factors.factors_use 61 <option value="SILAC (Lys+8, Arg+10)">SILAC (Lys+8, Arg+10)</option>
33 --special_factors="$factors.special_factors" 62 <option value="SILAC (Lys+8, Arg+10, Glu+6, Asp+5)">SILAC (Lys+8, Arg+10, Glu+6, Asp+5)</option>
34 #else 63 <!-- TODO: Add remaining SILAC options. -->
35 --special_factors="" 64 <option value="RABA +0,+6 (Peptide Labeled)">RABA +0,+6 (Peptide Labeled)</option>
36 #end if 65 <option value="Dimethyl +0,+4 (Peptide Labeled)">Dimethyl +0,+4 (Peptide Labeled)</option>
37 --search_foci="$search_foci" 66 <option value="Dimethyl +0,+6 (Peptide Labeled)">Dimethyl +0,+6 (Peptide Labeled)</option>
38 </command> 67 <option value="Dimethyl +0,+8 (Peptide Labeled)">Dimethyl +0,+8 (Peptide Labeled)</option>
39 <inputs> 68 <option value="Dimethyl +0,+4,+8 (Peptide Labeled)">Dimethyl +0,+4,+8 (Peptide Labeled)</option>
40 <param format="mgf" multiple="true" name="inputs" type="data" label="Peaklist (MGF)" help="" /> 69 <option value="Proteolytic O-18 labeling">Proteolytic O-18 labeling</option>
41 <param type="select" name="sample_type" label="Sample Type"> 70 <option value="Cleavable ICAT">Cleavable ICAT</option>
42 <option value="Identification">Identification</option> 71 <option value="ICPL Light, Heavy (Peptide Labeled)">ICPL Light, Heavy (Peptide Labeled)</option>
43 <option value="iTRAQ 4plex (Peptide Labeled)">iTRAQ 4plex (Peptide Labeled)</option> 72 <option value="ICPL Light, Heavy (Protein Labeled)">ICPL Light, Heavy (Protein Labeled)</option>
44 <option value="iTRAQ 4plex (Protein Labeled)">iTRAQ 4plex (Protein Labeled)</option> 73 <!-- TODO: Handle additional mTRAQ and iTRAQ options.
45 <option value="iTRAQ 8plex (Peptide Labeled)">iTRAQ 8plex (Peptide Labeled)</option> 74 handle TMT (doesn't seem like UI lets quantatate these)
46 <option value="iTRAQ 8plex (Protein Labeled)">iTRAQ 8plex (Protein Labeled)</option> 75 <UI_SAMPLE_TYPE>TMT6plex ID-only (Peptide Labeled)</UI_SAMPLE_TYPE>
47 <option value="TMT6plex ID-only (Peptide Labeled)">TMT6plex ID-only (Peptide Labeled)</option> 76 <UI_QUANT_TYPE></UI_QUANT_TYPE>
48 <option value="TMT6plex ID-only (Protein Labeled)">TMT6plex ID-only (Protein Labeled)</option> 77
49 <option value="TMT2plex ID-only (Peptide Labeled)">TMT2plex ID-only (Peptide Labeled)</option> 78 <UI_SAMPLE_TYPE></UI_SAMPLE_TYPE>
50 <option value="TMT ID-only (Peptide Labeled)">TMT ID-only (Peptide Labeled)</option> 79 <UI_QUANT_TYPE></UI_QUANT_TYPE>
51 <option value="mTRAQ (Peptide Labeled - M00, M04)">mTRAQ (Peptide Labeled - M00, M04)</option>
52 <option value="mTRAQ (Peptide Labeled - M00, M08)">mTRAQ (Peptide Labeled - M00, M08)</option>
53 <option value="mTRAQ (Peptide Labeled - M04, M08)">mTRAQ (Peptide Labeled - M04, M08)</option>
54 <option value="mTRAQ (Peptide Labeled - M00, M04, M08)">mTRAQ (Peptide Labeled - M00, M04, M08)</option>
55 <option value="SILAC (Lys+6, Arg+6)">SILAC (Lys+6, Arg+6)</option>
56 <option value="SILAC (Lys+4, Arg+10)">SILAC (Lys+4, Arg+10)</option>
57 <option value="SILAC (Lys+6, Arg+10)">SILAC (Lys+6, Arg+10)</option>
58 <option value="SILAC (Lys+8, Arg+10)">SILAC (Lys+8, Arg+10)</option>
59 <option value="SILAC (Lys+8, Arg+10, Glu+6, Asp+5)">SILAC (Lys+8, Arg+10, Glu+6, Asp+5)</option>
60 <!-- TODO: Add remaining SILAC options. -->
61 <option value="RABA +0,+6 (Peptide Labeled)">RABA +0,+6 (Peptide Labeled)</option>
62 <option value="Dimethyl +0,+4 (Peptide Labeled)">Dimethyl +0,+4 (Peptide Labeled)</option>
63 <option value="Dimethyl +0,+6 (Peptide Labeled)">Dimethyl +0,+6 (Peptide Labeled)</option>
64 <option value="Dimethyl +0,+8 (Peptide Labeled)">Dimethyl +0,+8 (Peptide Labeled)</option>
65 <option value="Dimethyl +0,+4,+8 (Peptide Labeled)">Dimethyl +0,+4,+8 (Peptide Labeled)</option>
66 <option value="Proteolytic O-18 labeling">Proteolytic O-18 labeling</option>
67 <option value="Cleavable ICAT">Cleavable ICAT</option>
68 <option value="ICPL Light, Heavy (Peptide Labeled)">ICPL Light, Heavy (Peptide Labeled)</option>
69 <option value="ICPL Light, Heavy (Protein Labeled)">ICPL Light, Heavy (Protein Labeled)</option>
70 <!-- TODO: Handle additional mTRAQ and iTRAQ options.
71 handle TMT (doesn't seem like UI lets quantatate these)
72 <UI_SAMPLE_TYPE>TMT6plex ID-only (Peptide Labeled)</UI_SAMPLE_TYPE>
73 <UI_QUANT_TYPE></UI_QUANT_TYPE>
74
75 <UI_SAMPLE_TYPE></UI_SAMPLE_TYPE>
76 <UI_QUANT_TYPE></UI_QUANT_TYPE>
77 80
78 <UI_SAMPLE_TYPE>TMT2plex ID-only (Peptide Labeled)</UI_SAMPLE_TYPE> 81 <UI_SAMPLE_TYPE>TMT2plex ID-only (Peptide Labeled)</UI_SAMPLE_TYPE>
79 <UI_QUANT_TYPE></UI_QUANT_TYPE> 82 <UI_QUANT_TYPE></UI_QUANT_TYPE>
80 83
81 <UI_SAMPLE_TYPE>TMT ID-only (Peptide Labeled)</UI_SAMPLE_TYPE> 84 <UI_SAMPLE_TYPE>TMT ID-only (Peptide Labeled)</UI_SAMPLE_TYPE>
82 <UI_QUANT_TYPE></UI_QUANT_TYPE> 85 <UI_QUANT_TYPE></UI_QUANT_TYPE>
83 --> 86 -->
84 <option value="SILAC unlabeled, N-15 labeled">SILAC unlabeled, N-15 labeled</option> 87 <option value="SILAC unlabeled, N-15 labeled">SILAC unlabeled, N-15 labeled</option>
85 </param> 88 </param>
86 <param type="select" name="cys_alkylation" label="Cys Alkylation"> 89 <param type="select" name="cys_alkylation" label="Cys Alkylation">
87 <option value="None">None</option> 90 <option value="None">None</option>
88 <option value="Iodoacetamide">Iodoacetamide</option> 91 <option value="Iodoacetamide">Iodoacetamide</option>
89 <option value="MMTS">MMTS</option> 92 <option value="MMTS">MMTS</option>
90 <option value="Acrylamide">Acrylamide</option> 93 <option value="Acrylamide">Acrylamide</option>
91 <option value="Iodoacetic acid">Iodoacetic acid</option> 94 <option value="Iodoacetic acid">Iodoacetic acid</option>
92 <option value="Iodoethanol">Iodoethanol</option> 95 <option value="Iodoethanol">Iodoethanol</option>
93 <option value="Vinylpyridine">Vinylpyridine</option> 96 <option value="Vinylpyridine">Vinylpyridine</option>
94 <option value="N-Ethylmaleimide">N-Ethylmaleimide</option> 97 <option value="N-Ethylmaleimide">N-Ethylmaleimide</option>
95 <option value="N-Methylmaleimide">N-Methylmaleimide</option> 98 <option value="N-Methylmaleimide">N-Methylmaleimide</option>
96 <option value="Iodoacetyl-PEO-Biotin">Iodoacetyl-PEO-Biotin</option> 99 <option value="Iodoacetyl-PEO-Biotin">Iodoacetyl-PEO-Biotin</option>
97 <option value="Iodoacetamide with Iodoacetyl-PEO-Biotin chase">Iodoacetamide with Iodoacetyl-PEO-Biotin chase</option> 100 <option value="Iodoacetamide with Iodoacetyl-PEO-Biotin chase">Iodoacetamide with Iodoacetyl-PEO-Biotin chase</option>
98 <option value="Iodoacetamide w other Cys mods possible">Iodoacetamide w other Cys mods possible</option> 101 <option value="Iodoacetamide w other Cys mods possible">Iodoacetamide w other Cys mods possible</option>
99 <option value="MMTS w other Cys mods possible">MMTS w other Cys mods possible</option> 102 <option value="MMTS w other Cys mods possible">MMTS w other Cys mods possible</option>
100 <option value="Unknown">Unknown</option> 103 <option value="Unknown">Unknown</option>
101 </param> 104 </param>
102 <param type="select" name="digestion" label="Digestion"> 105 <param type="select" name="digestion" label="Digestion">
103 <option value="Trypsin">Trypsin</option> 106 <option value="Trypsin">Trypsin</option>
104 <option value="Glu C">Glu C</option> 107 <option value="Glu C">Glu C</option>
105 <option value="Chymotrypsin">Chymotrypsin</option> 108 <option value="Chymotrypsin">Chymotrypsin</option>
106 <option value="CNBr">CNBr</option> 109 <option value="CNBr">CNBr</option>
107 <option value="Lys C">Lys C</option> 110 <option value="Lys C">Lys C</option>
108 <option value="Acid Cleavage">Acid Cleavage</option> 111 <option value="Acid Cleavage">Acid Cleavage</option>
109 <option value="Arg C">Arg C</option> 112 <option value="Arg C">Arg C</option>
110 <option value="Asp N">Asp N</option> 113 <option value="Asp N">Asp N</option>
111 <option value="Lys N">Lys N</option> 114 <option value="Lys N">Lys N</option>
112 <option value="Thermolysin">Thermolysin</option> 115 <option value="Thermolysin">Thermolysin</option>
113 <option value="Trypsin + Chymotrypsin">Trypsin + Chymotrypsin</option> 116 <option value="Trypsin + Chymotrypsin">Trypsin + Chymotrypsin</option>
114 <option value="Trypsin + Glu C">Trypsin + Glu C</option> 117 <option value="Trypsin + Glu C">Trypsin + Glu C</option>
115 <option value="Trypsin + Asp N">Trypsin + Asp N</option> 118 <option value="Trypsin + Asp N">Trypsin + Asp N</option>
116 <option value="Lys C + Chymotrypsin">Lys C + Chymotrypsin</option> 119 <option value="Lys C + Chymotrypsin">Lys C + Chymotrypsin</option>
117 <option value="Lys C + Glu C">Lys C + Glu C</option> 120 <option value="Lys C + Glu C">Lys C + Glu C</option>
118 <option value="Glu C + Asp N">Glu C + Asp N</option> 121 <option value="Glu C + Asp N">Glu C + Asp N</option>
119 <option value="Trypsin using MSIPI database">Trypsin using MSIPI database</option> 122 <option value="Trypsin using MSIPI database">Trypsin using MSIPI database</option>
120 <option value="None">None</option> 123 <option value="None">None</option>
121 </param> 124 </param>
122 <param type="select" name="instrument" label="Instrument"> 125 <param type="select" name="instrument" label="Instrument">
123 <option value="TripleTOF 5600">TripleTOF 5600</option> 126 <option value="TripleTOF 5600">TripleTOF 5600</option>
124 <option value="TripleTOF 4600">TripleTOF 4600</option> 127 <option value="TripleTOF 4600">TripleTOF 4600</option>
125 <option value="5800">5800</option> 128 <option value="5800">5800</option>
126 <option value="4800">4800</option> 129 <option value="4800">4800</option>
127 <option value="4700">4700</option> 130 <option value="4700">4700</option>
128 <option value="QSTAR Elite ESI">QSTAR Elite ESI</option> 131 <option value="QSTAR Elite ESI">QSTAR Elite ESI</option>
129 <option value="QSTAR Elite">QSTAR Elite</option> 132 <option value="QSTAR Elite">QSTAR Elite</option>
130 <option value="QSTAR oMALDI">QSTAR oMALDI</option> 133 <option value="QSTAR oMALDI">QSTAR oMALDI</option>
131 <option value="6500 QTRAP ESI">6500 QTRAP ESI</option> 134 <option value="6500 QTRAP ESI">6500 QTRAP ESI</option>
132 <option value="4500 QTRAP ESI">4500 QTRAP ESI</option> 135 <option value="4500 QTRAP ESI">4500 QTRAP ESI</option>
133 <option value="5500 QTRAP ESI">5500 QTRAP ESI</option> 136 <option value="5500 QTRAP ESI">5500 QTRAP ESI</option>
134 <option value="4000 QTRAP ESI">4000 QTRAP ESI</option> 137 <option value="4000 QTRAP ESI">4000 QTRAP ESI</option>
135 <option value="QTRAP ESI">QTRAP ESI</option> 138 <option value="QTRAP ESI">QTRAP ESI</option>
136 <option value="4000 QTRAP AP-MALDI">4000 QTRAP AP-MALDI</option> 139 <option value="4000 QTRAP AP-MALDI">4000 QTRAP AP-MALDI</option>
137 <option value="3200 QTRAP AP-MALDI">3200 QTRAP AP-MALDI</option> 140 <option value="3200 QTRAP AP-MALDI">3200 QTRAP AP-MALDI</option>
138 <option value="LTQ">LTQ</option> 141 <option value="LTQ">LTQ</option>
139 <option value="Orbi/FT MS (1-3ppm), LTQ MS/MS">Orbi/FT MS (1-3ppm), LTQ MS/MS</option> 142 <option value="Orbi/FT MS (1-3ppm), LTQ MS/MS">Orbi/FT MS (1-3ppm), LTQ MS/MS</option>
140 <option value="Orbi/FT MS (sub-ppm), LTQ MS/MS">Orbi/FT MS (sub-ppm), LTQ MS/MS</option> 143 <option value="Orbi/FT MS (sub-ppm), LTQ MS/MS">Orbi/FT MS (sub-ppm), LTQ MS/MS</option>
141 <option value="Orbi MS, Orbi MS/MS">Orbi MS, Orbi MS/MS</option> 144 <option value="Orbi MS, Orbi MS/MS">Orbi MS, Orbi MS/MS</option>
142 <option value="Orbi MS (sub-ppm), Orbi MS/MS">Orbi MS (sub-ppm), Orbi MS/MS</option> 145 <option value="Orbi MS (sub-ppm), Orbi MS/MS">Orbi MS (sub-ppm), Orbi MS/MS</option>
143 </param> 146 </param>
144 <conditional name="factors"> 147 <conditional name="factors">
145 <param name="factors_use" type="boolean" label="Specify Special Factors?" help="" truevalue="true" falsevalue="false" /> 148 <param name="factors_use" type="boolean" label="Specify Special Factors?" help="" truevalue="true" falsevalue="false" />
146 <when value="false" /> 149 <when value="false" />
147 <when value="true"> 150 <when value="true">
148 <param type="select" name="special_factors" label="Special Factors" display="checkboxes" multiple="true" help=""> 151 <param type="select" name="special_factors" label="Special Factors" display="checkboxes" multiple="true" help="">
149 <option value="Phosphorylation emphasis">Phosphorylation emphasis</option> 152 <option value="Phosphorylation emphasis">Phosphorylation emphasis</option>
150 <option value="Methyl esterification">Methyl esterification</option> 153 <option value="Methyl esterification">Methyl esterification</option>
151 <option value="Phos-Tyr affinity column">Phos-Tyr affinity column</option> 154 <option value="Phos-Tyr affinity column">Phos-Tyr affinity column</option>
152 <option value="Gel-based ID">Gel-based ID</option> 155 <option value="Gel-based ID">Gel-based ID</option>
153 <option value="Urea denaturation">Urea denaturation</option> 156 <option value="Urea denaturation">Urea denaturation</option>
154 <option value="Acetylation emphasis">Acetylation emphasis</option> 157 <option value="Acetylation emphasis">Acetylation emphasis</option>
155 <option value="Ubiquitin/SUMO enrichment">Ubiquitin/SUMO enrichment</option> 158 <option value="Ubiquitin/SUMO enrichment">Ubiquitin/SUMO enrichment</option>
156 <option value="BONCAT workflow">BONCAT workflow</option> 159 <option value="BONCAT workflow">BONCAT workflow</option>
157 <option value="PNGase F in O-18 water">PNGase F in O-18 water</option> 160 <option value="PNGase F in O-18 water">PNGase F in O-18 water</option>
158 <option value="Pronota">Pronota</option> 161 <option value="Pronota">Pronota</option>
159 <option value="O-methylisourea treatment">O-methylisourea treatment</option> 162 <option value="O-methylisourea treatment">O-methylisourea treatment</option>
160 <option value="Purified Histones">Purified Histones</option> 163 <option value="Purified Histones">Purified Histones</option>
161 <option value="Propionylation pre-digestion">Propionylation pre-digestion</option> 164 <option value="Propionylation pre-digestion">Propionylation pre-digestion</option>
162 <option value="Propionylation post-digestion">Propionylation post-digestion</option> 165 <option value="Propionylation post-digestion">Propionylation post-digestion</option>
163 <option value="Deuteroacetylation pre-digestion">Deuteroacetylation pre-digestion</option> 166 <option value="Deuteroacetylation pre-digestion">Deuteroacetylation pre-digestion</option>
164 <option value="Deuteroacetylation post-digestion">Deuteroacetylation post-digestion</option> 167 <option value="Deuteroacetylation post-digestion">Deuteroacetylation post-digestion</option>
165 <option value="Iodo and Thyroxine mods enrichment">Iodo and Thyroxine mods enrichment</option> 168 <option value="Iodo and Thyroxine mods enrichment">Iodo and Thyroxine mods enrichment</option>
166 </param> 169 </param>
167 </when> 170 </when>
168 </conditional> 171 </conditional>
169 <param format="fasta" name="database" type="data" label="Database" /> 172 <param format="fasta" name="database" type="data" label="Database" />
170 <param name="quantitative" type="boolean" truevalue="True" falsevalue="False" label="Run Quantitation (if applicable)" checked="False" help="" /> 173 <param name="quantitative" type="boolean" truevalue="True" falsevalue="False" label="Run Quantitation (if applicable)" checked="False" help="" />
171 <param name="background_correction" type="boolean" truevalue="True" falsevalue="False" label="Use Background Correction (if applicable)" checked="False" help="" /> 174 <param name="background_correction" type="boolean" truevalue="True" falsevalue="False" label="Use Background Correction (if applicable)" checked="False" help="" />
172 <param name="bias_correction" type="boolean" truevalue="True" falsevalue="False" label="Use Bias Correction (if applicable)" checked="False" help="" /> 175 <param name="bias_correction" type="boolean" truevalue="True" falsevalue="False" label="Use Bias Correction (if applicable)" checked="False" help="" />
173 <param type="select" name="search_foci" label="Search Focus" display="checkboxes" multiple="true" help=""> 176 <param type="select" name="search_foci" label="Search Focus" display="checkboxes" multiple="true" help="">
174 <option value="Biological modifications">Biological modifications</option> 177 <option value="Biological modifications">Biological modifications</option>
175 <option value="Amino acid substitutions">Amino acid substitutions</option> 178 <option value="Amino acid substitutions">Amino acid substitutions</option>
176 </param> 179 </param>
177 <param name="search_effort" type="boolean" truevalue="Thorough" falsevalue="Rapid" label="Thorough Search" checked="True" help="" /> 180 <param name="search_effort" type="boolean" truevalue="Thorough" falsevalue="Rapid" label="Thorough Search" checked="True" help="" />
178 <param name="pspep" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Use PSPEP" checked="True" help="" /> 181 <param name="pspep" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Use PSPEP" checked="True" help="" />
179 <param type="select" name="min_unused_protscore" label="Detected Protein Threshold [Unused ProtScore (Conf)]"> 182 <param type="select" name="min_unused_protscore" label="Detected Protein Threshold [Unused ProtScore (Conf)]">
180 <option value="3.0">3.0 (99.9)</option> 183 <option value="3.0">3.0 (99.9)</option>
181 <option value="2.0">2.0 (99.0%)</option> 184 <option value="2.0">2.0 (99.0%)</option>
182 <option value="1.3">1.3 (95.0%)</option> 185 <option value="1.3">1.3 (95.0%)</option>
183 <option value="1.0">1.0 (90.0%)</option> 186 <option value="1.0">1.0 (90.0%)</option>
184 <option value="0.70">0.70 (80.0%)</option> 187 <option value="0.70">0.70 (80.0%)</option>
185 <option value="0.47">0.47 (66.0%)</option> 188 <option value="0.47">0.47 (66.0%)</option>
186 <option value="0.10">0.10 (20.0%)</option> 189 <option value="0.10">0.10 (20.0%)</option>
187 <option value="0.05" selected="true">0.05 (10.0%)</option> 190 <option value="0.05" selected="true">0.05 (10.0%)</option>
188 </param> 191 </param>
189 </inputs> 192 </inputs>
190 <outputs> 193 <outputs>
191 <data format="group" name="output" label="ProteinPilot results for ${on_string}"/> 194 <data format="group" name="output" label="ProteinPilot results for ${on_string}"/>
192 <data format="xml" name="output_methods" label="ProteinPilot methods xml for ${on_string}" /> 195 <data format="xml" name="output_methods" label="ProteinPilot methods xml for ${on_string}" />
193 <data format="xlsx" name="output_pspep_report" label="ProteinPilot PSPEP Report for ${on_string}"> 196 <data format="xlsx" name="output_pspep_report" label="ProteinPilot PSPEP Report for ${on_string}">
194 <filter>pspep</filter> 197 <filter>pspep</filter>
195 </data> 198 </data>
196 </outputs> 199 </outputs>
197 <help> 200 <help>
198 </help> 201 <![CDATA[
202
203 ]]>
204 </help>
199 </tool> 205 </tool>