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