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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 #end if
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25 </command>
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26 <requirements>
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27 <requirement type="set_environment">INSTALL_RUN_PATH</requirement>
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28 <requirement type="package" version="3.2.1">package_r_3_2_1</requirement>
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29 </requirements>
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30 <inputs>
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31 <param type="select" name="type" label="MaxQuant or Scaffold">
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32 <option value="MaxQuant">MaxQuant</option>
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33 <option value="Scaffold">Scaffold</option>
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34 </param>
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35 <param format="dat" name="input" type="data" label="Scaffold or MaxQuant proteinGroup Output"/>
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36 <param type="boolean" name="preybool" checked="true" label="Create Prey File"/>
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37 <param type="data" name="fasta_db" format="fasta" label="Provide Uniprot Fasta database" optional="true"/>
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38 <param name="bait_bool" type="boolean" checked="true" label="Are You Providing Your Own bait file?"/>
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39 <param type="data" format="dat" name="bait_file_in" label="Bait File" optional="true"/>
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40 <repeat name="bait" title="Bait Create">
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41 <param name="bait1" type="text" size="100" label="Bait"/>
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42 <param name="assign" type="text" size="100" label="Group Assignment"/>
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43 <param name="T_C" type="boolean" checked="true" label="Is this a Control?"/>
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44 </repeat>
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45
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46 </inputs>
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47 <outputs>
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48 <data format="txt" name="Inter_file" label="Inter File"/>
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49 <data format="txt" name="Prey_file" label="Prey File" />
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50 <data format="txt" name="Bait_file" label="Bait File" />
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51 </outputs>
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52 <stdio>
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53 <regex match="Error|error"
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54 source="stdout"
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55 level="fatal"
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56 description="Unknown error"/>
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57 <regex match="Error|error"
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58 source="stderr"
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59 level="fatal"
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60 description="Unknown error"/>
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61 <regex match="Error: bad bait"
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62 source="stdout"
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63 level="fatal"
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64 description="Error: bad bait"/>
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65 </stdio>
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66
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67 <tests>
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68 <test>
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69 <param name="input" value="fa_gc_content_input.fa"/>
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70 <output name="out_file1" file="fa_gc_content_output.txt"/>
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71 </test>
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72 </tests>
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73 <help>
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74 Pre-Processing
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75 ==============
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76
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77 --------------
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20
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78
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79 This tool will read in a Scaffold *Samples Report* file (tab-delimited
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80 txt file) or a MaxQuant *peptides.txt* file and process them to generate
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81 a *Bait File, Prey File,* and *Inter File* for SAINTexpress analysis.
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20
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82
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83 1) MaxQuant or Scaffold
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84 -----------------------
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85
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86 APOSTL is able to recognize either a Scaffold *Samples Report* file
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87 (tab-delimited txt file) or the *peptides.txt* file output in the
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88 MaxQuant *txt* output folder. No modifications should be made to these
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89 files. Please designate which one is being provided.
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20
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90
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91 2) Scaffold or MaxQuant File Input
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92 ----------------------------------
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93
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94 Select the corresponding *Samples Report* or *peptides.txt* here.
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95
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96 3) Create Prey File
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97 -------------------
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98
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99 Select whether or not you would like APOSTL to generate a prey file.
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100
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101 When making a prey file, APOSTL queries a user provided FASTA database
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102 (see below) in order to extract protein amino acid lengths and gene
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103 names. This may take several minutes depending on your computer and if
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104 your Galaxy distribution is cluster enabled. Some users may want to run
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105 SAINTexpress using the same data set while changing which baits are
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106 considered test or control. It is useful to toggle **Create Prey File**
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107 off in order to save time by circumventing this step as the same prey
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108 file can be used for both SAINTexpress runs.
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20
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109
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110 4) Provide Uniprot FASTA database
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111 ---------------------------------
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112
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113 Please specify a FASTA file containing the protein sequence. You can
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114 download the latest release of Uniprot's reviewed sequences (Swiss-Prot)
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115 at http://www.uniprot.org/downloads. For computing efficiency,
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116 please limit your FASTA file to your species of interest. It is
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117 generally advised to use the same FASTA database that was used for your
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118 database searches during peptide and protein ID.
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119
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120 5) Are You Providing Your Own Bait File?
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121 ----------------------------------------
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122
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123 Users have two options for providing a *Bait* file. If you would like to
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124 create your own *Bait* file, select Yes and designate the file below. If
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125 you would like to use the **Bait Create** tool to create a *Bait* file
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126 within Galaxy, please select No and proceed to the **Bait Create** tool.
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127
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128 6) Bait File
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129 ------------
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130
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131 If you selected Yes above, please specify the *Bait* file you would like
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132 to provide. If you selected No above, ignore this argument and proceed
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133 to the **Bait Create** tool.
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134
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135 **Note:** Individual bait names must match to the sample names
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136 within your Scaffold or MaxQuant output exactly and must contain no
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137 whitespace characters (e.g. spaces) or dashes.
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138
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139 7) Bait Create
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140 --------------
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141
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142 Using the **Bait Create** tool, you can create your *bait.txt* file.
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20
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143
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144 **Note:** Individual bait names must match to the sample names
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145 within your Scaffold or MaxQuant output exactly and must contain no
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146 whitespace characters (e.g. spaces) or dashes.
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147
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148 APOSTL uses this bait file to find the user's baits of interest within a
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149 *Samples Report* or *peptides.txt* file and when preparing the
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150 *inter.txt* file.
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20
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151
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152 --------------
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153
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154 Once your parameters have been finalized, please press the Execute
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155 button to start processing. This may take a few minutes. Once your
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156 process has been completed, you will see your *Bait File, Prey File,*
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157 and *Inter File* on the right hand side of your panel highlighted in
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158 green.
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159 </help>
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160 </tool>
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