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1 <tool id="SAINT_preprocessing_v5" name="SAINT pre-processing">
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2 <description></description>
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3 <command interpreter="python">
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4 #if (str($type) == 'Scaffold'):
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5 SAINT_preprocessing.py $input $preybool $fasta_db $Inter_file $Prey_file
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6 "
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7 #for $ba in $bait
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8 ${ba.bait1}
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9 ${ba.assign}
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10 ${ba.T_C}
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11 #end for
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12 "
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13 $Bait_file \$INSTALL_RUN_PATH/ $bait_bool $bait_file_in
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14 #elif (str($type) == 'MaxQuant'):
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15 SAINT_preprocessing_mq_pep.py $input $preybool $fasta_db $Inter_file $Prey_file
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16 "
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17 #for $ba in $bait
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18 ${ba.bait1}
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19 ${ba.assign}
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20 ${ba.T_C}
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21 #end for
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22 "
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23 $Bait_file \$INSTALL_RUN_PATH/ $bait_bool $bait_file_in
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24 #elif (str($type) == 'Peptideshaker'):
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25 Protein_report_processing.py "$input" $Bait_file $use_metric $fasta_db $preybool
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26 "
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27 #for $ba in $bait
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28 ${ba.bait1}
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29 ${ba.assign}
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30 ${ba.T_C}
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31 #end for
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32 "
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33 \$INSTALL_RUN_PATH/ $bait_bool $bait_file_in $Inter_file $Prey_file
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34 #end if
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35 </command>
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36 <requirements>
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37 <requirement type="set_environment">INSTALL_RUN_PATH</requirement>
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38 </requirements>
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39 <inputs>
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40 <conditional name="type_select">
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41 <param type="select" name="type" label="MaxQuant or Scaffold">
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42 <option value="MaxQuant">MaxQuant</option>
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43 <option value="Scaffold">Scaffold</option>
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44 <option value="Peptideshaker">Peptideshaker</option>
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45 </param>
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46 <when value="MaxQuant">
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47 <param format="dat" name="input" type="data" label="MaxQuant peptides Output"/>
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48 <param type="boolean" name="preybool" checked="true" label="Create Prey File"/>
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49 <param type="data" name="fasta_db" format="fasta" label="Provide Uniprot Fasta database" optional="true"/>
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50 <param name="bait_bool" type="boolean" checked="true" label="Are You Providing Your Own bait file?"/>
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51 <param type="data" format="dat" name="bait_file_in" label="Bait File" optional="true"/>
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52 <repeat name="bait" title="Bait Create">
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53 <param name="bait1" type="text" size="100" label="Bait"/>
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54 <param name="assign" type="text" size="100" label="Group Assignment"/>
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55 <param name="T_C" type="boolean" checked="true" label="Is this a Control?"/>
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56 </repeat>
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57 <when value="Scaffold">
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58 <param format="dat" name="input" type="data" label="Scaffold Output"/>
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59 <param type="boolean" name="preybool" checked="true" label="Create Prey File"/>
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60 <param type="data" name="fasta_db" format="fasta" label="Provide Uniprot Fasta database" optional="true"/>
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61 <param name="bait_bool" type="boolean" checked="true" label="Are You Providing Your Own bait file?"/>
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62 <param type="data" format="dat" name="bait_file_in" label="Bait File" optional="true"/>
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63 <repeat name="bait" title="Bait Create">
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64 <param name="bait1" type="text" size="100" label="Bait"/>
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65 <param name="assign" type="text" size="100" label="Group Assignment"/>
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66 <param name="T_C" type="boolean" checked="true" label="Is this a Control?"/>
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67 </repeat>
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68 </when>
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69 <when value="Peptideshaker">
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70 <param format="dat" name="input" type="data" label="Peptideshaker Output" multiple="true"/>
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71 <param type="select" name="use_metric" label="Select Report File Value for Quantification">
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72 <option value="Validated_Peptides">#Validated Peptides</option>
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73 <option value="Peptides">#Peptides</option>
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74 <option value="Unique">#Unique</option>
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75 <option value="Validated_PSMs">#Validated PSMs</option>
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76 <option value="PSMs">#PSMs</option>
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77 </param>
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78 <param type="boolean" name="preybool" checked="true" label="Create Prey File"/>
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79 <param type="data" name="fasta_db" format="fasta" label="Provide Uniprot Fasta database" optional="true"/>
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80 <param name="bait_bool" type="boolean" checked="true" label="Are You Providing Your Own bait file?"/>
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81 <param type="data" format="dat" name="bait_file_in" label="Bait File" optional="true"/>
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82 <repeat name="bait" title="Bait Create">
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83 <param name="bait1" type="text" size="100" label="Bait"/>
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84 <param name="assign" type="text" size="100" label="Group Assignment"/>
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85 <param name="T_C" type="boolean" checked="true" label="Is this a Control?"/>
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86 </repeat>
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87 </when>
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88 </conditional>
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89 </inputs>
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90 <outputs>
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91 <data format="txt" name="Inter_file" label="Inter File"/>
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92 <data format="txt" name="Prey_file" label="Prey File" />
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93 <data format="txt" name="Bait_file" label="Bait File" />
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94 </outputs>
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95 <stdio>
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96 <regex match="Error: bad bait"
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97 source="stdout"
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98 level="fatal"
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99 description="Error: bad bait"/>
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100 <regex match="IOError: [Errno 2] No such file or directory: './tukeys_output.txt'"
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101 source="stderr"
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102 level="fatal"
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103 description="Error: Scaffold/MaxQuant mismatch. Check job settings."/>
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104 <regex match="bait_temp_file = open(sys.argv[10], 'r')"
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105 source="stderr"
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106 level="fatal"
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107 description="Error: Bait create settings mismatch. Check job settings."/>
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108 <regex match="Error|error"
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109 source="stdout"
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110 level="fatal"
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111 description="Unknown error"/>
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112 <regex match="Error|error"
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113 source="stderr"
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114 level="fatal"
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115 description="Unknown error"/>
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116 </stdio>
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117
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118 <tests>
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119 <test>
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120 <param name="input" value="fa_gc_content_input.fa"/>
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121 <output name="out_file1" file="fa_gc_content_output.txt"/>
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122 </test>
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123 </tests>
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124 <help>
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125 Pre-Processing
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126 ^^^^^^^^^^^^^^
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127
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128 This tool will read in a Scaffold *Samples Report* file (tab-delimited
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129 txt file), multiple Peptideshaker *Protein Report* files or a MaxQuant
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130 *peptides.txt* file and process them to generate a *Bait File, Prey
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131 File,* and *Inter File* for SAINTexpress analysis.
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132
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133 --------------
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134
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135 **1) MaxQuant or Scaffold**
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136
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137 APOSTL is able to recognize either a Scaffold *Samples Report* file
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138 (tab-delimited txt file) or the *peptides.txt* file output in the
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139 MaxQuant *txt* output folder. No modifications should be made to these
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140 files. Please designate which one is being provided.
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141
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142 **2) Scaffold or MaxQuant File Input**
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143
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144 Select the corresponding *Samples Report* or *peptides.txt* here.
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145
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146 **3) Create Prey File**
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147
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148 Select whether or not you would like APOSTL to generate a prey file.
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149
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150 When making a prey file, APOSTL queries a user provided FASTA database
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151 (see below) in order to extract protein amino acid lengths and gene
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152 names. This may take several minutes depending on your computer and if
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153 your Galaxy distribution is cluster enabled. Some users may want to run
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154 SAINTexpress using the same data set while changing which baits are
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155 considered test or control. It is useful to toggle **Create Prey File**
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156 off in order to save time by circumventing this step as the same prey
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157 file can be used for both SAINTexpress runs.
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158
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159 **4) Provide Uniprot FASTA database**
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160
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161 Please specify a FASTA file containing the protein sequence. You can
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162 download the latest release of Uniprot's reviewed sequences (Swiss-Prot)
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163 http://www.uniprot.org/downloads. For computing efficiency,
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164 please limit your FASTA file to your species of interest. It is
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165 generally advised to use the same FASTA database that was used for your
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166 database searches during peptide and protein ID.
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167
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168 **5) Are You Providing Your Own Bait File?**
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169
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170 Users have two options for providing a *Bait* file. If you would like to
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171 create your own *Bait* file, select Yes and designate the file below. If
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172 you would like to use the **Bait Create** tool to create a *Bait* file
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173 within Galaxy, please select No and proceed to the **Bait Create** tool.
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174
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175 **6) Bait File**
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176
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177 If you selected Yes above, please specify the *Bait* file you would like
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178 to provide. If you selected No above, ignore this argument and proceed
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179 to the **Bait Create** tool.
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180
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181 **Note:** Individual bait names must match to the sample names
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182 within your Scaffold or MaxQuant output exactly and must contain no
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183 whitespace characters (e.g. spaces) or dashes.
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184
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185 **Note:** When using Peptideshaker output the baits in the baitfile
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186 need to be in the same order as the files selected.
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187
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188 **7) Bait Create**
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189
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190 Using the **Bait Create** tool, you can create your *bait.txt* file.
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191
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192 **Note:** Individual bait names must match to the sample names
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193 within your Scaffold or MaxQuant output exactly and must contain no
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194 whitespace characters (e.g. spaces) or dashes.
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195
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196 APOSTL uses this bait file to find the user's baits of interest within a
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197 *Samples Report* or *peptides.txt* file and when preparing the
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198 *inter.txt* file.
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199
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200 --------------
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201
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202 Once your parameters have been finalized, please press the Execute
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203 button to start processing. This may take a few minutes. Once your
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204 process has been completed, you will see your *Bait File, Prey File,*
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205 and *Inter File* on the right hand side of your panel highlighted in
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206 green.
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207 </help>
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208 </tool>
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