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