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1 <tool id="peptide_shaker" name="Peptide Shaker" version="0.1.0">
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2 <!-- TODO: Set defaults for weights correctly -->
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3 <description>
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4 Peform protein identification combining X! Tandem and OMSSA (using SearchGUI) and PeptideShaker pipeline.
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5 </description>
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6 <command>
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7 #from datetime import datetime
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8 #set $exp_str = "Galaxy Experiment %s" % datetime.now().strftime("%Y%m%d%H%M%s")
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9 #set $samp_str = "Sample %s" % datetime.now().strftime("%Y%m%d%H%M%s")
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10 mkdir spectra;
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11 mkdir output;
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12 mkdir output_reports;
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13 cwd=`pwd`;
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14 #for $mgf in $peak_lists:
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15 #set $input_name = $mgf.display_name.replace(".mgf", "") + ".mgf"
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16 ln -s '$mgf' 'spectra/$input_name';
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17 #end for
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18 SearchCLI \
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19 -spectrum_files \$cwd/spectra \
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20 -output_folder \$cwd/output \
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21 -ppm $precursor_ion_tol_units \
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22 -prec_tol $precursor_ion_tol \
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23 -frag_tol $fragment_tol \
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24 -enzyme '$enzyme' \
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25 #set $fixed_mods_str = $fixed_modifications or ''
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26 #set $variable_mods_str = $variable_modifications or ''
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27 #if $fixed_mods_str
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28 -fixed_mods "$fixed_mods_str" \
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29 #end if
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30 #if $variable_mods_str
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31 -variable_mods "$variable_mods_str" \
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32 #end if
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33 -mc $missed_cleavages \
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34 #if $advanced.specify:
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35 -xtandem $advanced.xtandem \
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36 #if $advanced.omssa.run_omssa
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37 #set $omssa = 1
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38 #else
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39 #set $omssa = 0
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40 #end if
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41 -omssa $omssa \
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42 #if $omssa == 1
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43 -hitlist_length ${advanced.omssa.hitlist_length} \
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44 -remove_prec ${advanced.omssa.remove_precursor} \
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45 -scale_prec ${advanced.omssa.scale_precursor} \
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46 -estimate_charge ${advanced.omssa.estimate_charge} \
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47 #end if
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48 #end if
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49 -db $input_database;
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50 PeptideShakerCLI \
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51 -experiment '$exp_str' \
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52 -sample '$samp_str' \
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53 -replicate 1 \
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54 -spectrum_files \$cwd/spectra \
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55 -identification_files \$cwd/output \
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56 -search_params \$cwd/output/SearchGUI.parameters \
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57 -out_txt_1 \$cwd/output_reports \
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58 #if $processing_options.specify
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59 -protein_FDR ${processing_options.protein_fdr} \
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60 -peptide_FDR ${processing_options.peptide_fdr} \
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61 -psm_FDR ${processing_options.psm_fdr} \
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62 -psm_FLR ${processing_options.psm_flr} \
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63 #if str($processing_options.a_score.use) == "1"
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64 #set $a_score = 1
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65 #else
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66 #set $a_score = 0
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67 #end if
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68 -a_score $a_score \
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69 #if str($a_score) == "1"
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70 -a_score_neutral_losses ${processing_options.a_score.neutral_losses} \
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71 #end if
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72 #end if
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73 #if $filtering_options.specify
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74 -min_peptide_length ${filtering_options.min_peptide_length} \
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75 -max_peptide_length ${filtering_options.max_peptide_length} \
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76 -max_precursor_error ${filtering_options.max_precursor_error} \
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77 -max_precursor_error_type ${filtering_options.max_precursor_error_type} \
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78 -max_xtandem_e ${filtering_options.max_xtandem_e} \
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79 -max_omssa_e ${filtering_options.max_omssa_e} \
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80 -exclude_unknown_ptms ${filtering_options.exclude_unknown_ptms} \
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81 #end if
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82 -out \$cwd/output.cps ;
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83 mv output_reports/*peptides.txt peptides.txt ;
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84 mv output_reports/*psms.txt psms.txt ;
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85 mv output_reports/*proteins.txt proteins.txt
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86 </command>
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87 <stdio>
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88 <exit_code range="1:" level="fatal" description="Job Failed" />
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89 </stdio>
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90 <inputs>
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91 <param format="fasta" name="input_database" type="data" label="Protein Database" help="Select FASTA database from history. Typically, a target-decoy database is incorporated into the Scaffold engine for FDR analysis"/>
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92 <param format="mgf" name="peak_lists" type="data" multiple="true" label="Input Peak Lists (mgf)" help="Select appropriate MGF dataset(s) from history" />
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93 <param name="precursor_ion_tol_units" type="select" label="Precursor Ion Tolerance Units" help="Select based on instrument used, as different machines provide different quality of spectra. ppm is a standard for most precursor ions">
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94 <option value="1">Parts per million (ppm)</option>
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95 <option value="0">Daltons</option>
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96 </param>
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97 <param name="precursor_ion_tol" type="float" value="10" label="Percursor Ion Tolerance" help="Provide error value for precursor ion, based on instrument used. 10 ppm recommended for Orbitrap instrument"/>
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98 <param name="fragment_tol" type="float" value="0.5" label="Fragment Tolerance (Daltons)" help="Provide error value for fragment ions, based on instrument used"/>
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99 <param name="enzyme" type="select" label="Enzyme" help="Which enzyme was used for protein digest in experiment? In most cases, trypsin is used">
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100 <option value="Trypsin">Trypsin</option>
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101 <option value="Arg-C">Arg-C</option>
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102 <option value="CNBr">CNBr</option>
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103 <option value="Chymotrypsin (FYWL)">Chymotrypsin (FYWL)</option>
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104 <option value="Formic Acid">Formic Acid</option>
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105 <option value="Lys-C">Lys-C</option>
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106 <option value="Lys-C, no P rule">Lys-C, no P rule</option>
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107 <option value="Pepsin A">Pepsin A</option>
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108 <option value="Trypsin + CNBr">Trypsin + CNBr</option>
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109 <option value="Trypsin + Chymotrypsin (FYWLKR)">Trypsin + Chymotrypsin (FYWLKR)</option>
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110 <option value="Trypsin, no P rule">Trypsin, no P rule</option>
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111 <option value="whole protein">whole protein</option>
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112 <option value="Asp-N">Asp-N</option>
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113 <option value="Glu-C">Glu-C</option>
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114 <option value="Asp-N + Glu-C">Asp-N + Glu-C</option>
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115 <option value="Top-Down">Top-Down</option>
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116 <option value="Semi-Tryptic">Semi-Tryptic</option>
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117 <option value="No enzyme">No enzyme</option>
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118 <option value="Chymotrypsin, no P rule (FYWL)">Chymotrypsin, no P rule (FYWL)</option>
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119 <option value="Asp-N (DE)">Asp-N (DE)</option>
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120 <option value="Glu-C (DE)">Glu-C (DE)</option>
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121 <option value="Lys-N (K)">Lys-N (K)</option>
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122 <option value="Thermolysin, no P rule">Thermolysin, no P rule</option>
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123 <option value="Semi-Chymotrypsin (FYWL)">Semi-Chymotrypsin (FYWL)</option>
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124 <option value="Semi-Glu-C">Semi-Glu-C</option>
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125 </param>
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126 <param name="missed_cleavages" type="integer" value="2" label="Maximum Missed Cleavages" help="Allow peptides to contain up to this many missed enzyme cleavage sites. 2 is the recommended value"/>
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127 <param name="fixed_modifications" type="select" label="Fixed Modifications" multiple="true" help="Occurs in known places on peptide sequence. Hold the appropriate key while clicking to select multiple items">
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128 <options from_file="searchgui_mods.loc">
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129 <column name="name" index="0" />
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130 <column name="value" index="0" />
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131 </options>
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132 </param>
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133 <param name="variable_modifications" type="select" label="Variable Modifications" multiple="true" help="Can occur anywhere on the peptide sequence; adds additional error to search score. Hold the appropriate key while clicking to select multiple items">
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134 <options from_file="searchgui_mods.loc">
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135 <column name="name" index="0" />
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136 <column name="value" index="0" />
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137 </options>
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138 </param>
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139 <param name="min_charge" label="Minimum Charge" value="2" type="integer" help="Lowest searched charge value for fragment ions"/>
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140 <param name="max_charge" label="Maximum Charge" value="4" type="integer" help="Highest searched charge value for fragment ions"/>
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141 <param name="forward_ion" label="Forward Ion" type="select" help="Searched fragment ion type. Select a, b or c based on collisions induced in experiment">
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142 <option value="a">a</option>
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143 <option value="b" selected="true">b</option>
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144 <option value="c">c</option>
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145 </param>
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146 <param name="reverse_ion" label="Reverse Ion" type="select" help="Searched fragment ion type. Select x, y, or z based on collisions induced in experiment">
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147 <option value="x">x</option>
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148 <option value="y" selected="true">y</option>
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149 <option value="z">z</option>
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150 </param>
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151 <conditional name="advanced">
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152 <param name="specify" label="Specify Advanced Search Options" type="boolean" truevalue="true" falsevalue="false" help=" Run X! Tandem, OMSSA, or both and provide options for OMSSA search"/>
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153 <when value="false" />
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154 <when value="true">
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155 <param name="xtandem" label="Run X! Tandem" type="boolean" truevalue="1" falsevalue="0" checked="true" />
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156 <conditional name="omssa">
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157 <param name="run_omssa" label="Run OMSSA" type="boolean" truevalue="1" falsevalue="0" checked="true" />
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158 <when value="0" />
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159 <when value="1">
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160 <param name="hitlist_length" label="OMSSA: Hit List Length" type="integer" value="25" />
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161 <param name="remove_precursor" label="OMSSA: Remove Precurosr" type="boolean" truevalue="1" falsevalue="0" checked="true"/>
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162 <param name="scale_precursor" label="OMSSA: Scale Precursor Mass" type="boolean" truevalue="1" falsevalue="0" checked="false"/>
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163 <param name="estimate_charge" label="OMSSA: Estimate Charge" type="boolean" truevalue="1" falsevalue="0" checked="true" />
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164 </when>
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165 </conditional>
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166 </when>
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167 </conditional>
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168 <conditional name="processing_options">
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169 <param name="specify" label="Specify Advanced PeptideShaker Processing Options" type="boolean" truevalue="true" falsevalue="false" help="Select and provide False Discovery Rate (FDR) levels at the peptide, protein, and peptide-spectral match (PSM) levels, as well as False Loss Rate (FLR) for PSM’s and A score options for post-translational modifications (PTM’s). See this link_ for more details
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170
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171 .. _link: http://peptide-shaker.googlecode.com/svn-history/r1267/wiki/tutorial/6_ptm_analysis.docx" />
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172 <when value="false" />
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173 <when value="true">
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174 <param name="protein_fdr" label="FDR at the protein level" help="In percent (default 1% FDR: '1')" value="1" type="float" />
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175 <param name="peptide_fdr" label="FDR at the peptide level" help="In percent (default 1% FDR: '1')" value="1" type="float" />
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176 <param name="psm_fdr" label="FDR at the PSM level" help="In percent (default 1% FDR: '1')" value="1" type="float" />
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177 <param name="psm_flr" label="FLR at the PSM level" help="In percent (default 1% FLR: '1'). Percent for peptides with different potential modification sites and one variable modification." value="1" type="float" />
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178 <conditional name="a_score">
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179 <param name="use" label="Calculate A Score" type="boolean" truevalue="1" falsevalue="0" checked="true" />
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180 <when value="0" />
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181 <when value="1">
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182 <param name="neutral_losses" label="Include Neutral Losses in A Score" type="boolean" truevalue="1" falsevalue="0" />
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183 </when>
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184 </conditional>
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185 <!-- SKIPPING -protein_fraction_mw_confidence ${processing_options.protein_fraction_mw_confidence} -->
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186 </when>
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187 </conditional>
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188 <conditional name="filtering_options">
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189 <param name="specify" label="Specify Advanced PeptideShaker Filtering Options" type="boolean" truevalue="true" falsevalue="false" help="Filter based on peptide lengths, precursor mass error, E value errors from X! Tandem and OMSSA, and include/exclude unknown PTM’s"/>
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190 <when value="false" />
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191 <when value="true">
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192 <param name="min_peptide_length" label="Minimum Peptide Length" value="6" type="integer" />
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193 <param name="max_peptide_length" label="Maximum Peptide Length" value="30" type="integer" />
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194 <param name="max_precursor_error" label="Maximum Precursor Error" value="10" type="float" help="Next option specifies units (Da or ppm)." />
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195 <param name="max_precursor_error_type" label="Maximum Precursor Error Type" type="select">
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196 <option value="0">ppm</option>
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197 <option value="1">Daltons</option>
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198 </param>
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199 <param name="max_xtandem_e" label="Maximum X! Tandem E Value" value="100" type="float" help="" />
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200 <param name="max_omssa_e" label="Maximum OMSSA E Value" value="100" type="float" help="" />
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201 <param name="exclude_unknown_ptms" label="Exclude Unknown PTMs" type="boolean" truevalue="1" falsevalue="0" checked="true" />
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202 </when>
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203 </conditional>
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204 </inputs>
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205 <outputs>
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206 <data format="cps" name="output" label="PeptideShaker CPS results for ${on_string}" from_work_dir="output.cps" />
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207 <data format="tabular" name="output_peptides" label="PeptideShaker Peptide Report for ${on_string}" from_work_dir="peptides.txt" />
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208 <data format="tabular" name="output_proteins" label="PeptideShaker Protein Report for ${on_string}" from_work_dir="proteins.txt" />
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209 <data format="tabular" name="output_psms" label="PeptideShaker PSM Report for ${on_string}" from_work_dir="psms.txt" />
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210 </outputs>
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211 <requirements>
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212 <requirement type="package" version="0.20.1">PeptideShaker</requirement>
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213 <requirement type="package" version="1.14.1">SearchGUI</requirement>
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214 </requirements>
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215 <help>
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216 **What it does**
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217
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218 Runs multiple search engines (X! Tandem and OMSSA) on any number of MGF peak lists using the SearchGUI application and combines the results.
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219
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220 ------
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221
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222 **Citation**
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223
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224 For the underlying tool, please cite `TODO`
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225
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226 If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-peptideshaker
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227 </help>
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228 </tool>
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