Mercurial > repos > bornea > saint_preprocessing_peptideshaker

comparison Protein_report_processing.xml @ 12:ad33728cecc0 draft

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author bornea
date Tue, 23 Aug 2016 20:03:58 -0400
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11:6d61b698125d 12:ad33728cecc0
12 </command> 12 </command>
13 <requirements> 13 <requirements>
14 <requirement type="set_environment">INSTALL_RUN_PATH</requirement> 14 <requirement type="set_environment">INSTALL_RUN_PATH</requirement>
15 </requirements> 15 </requirements>
16 <inputs> 16 <inputs>
17 <param format="dat" name="input" type="data" label="Scaffold or MaxQuant peptides Output" multiple="true"/> 17 <param format="dat" name="input" type="data" label="Peptideshaker Output" multiple="true"/>
18 <param type="select" name="use_metric" label="Select Report File Value for Qunatification"> 18 <param type="select" name="use_metric" label="Select Report File Value for Quantification">
19 <option value="Validated_Peptides">#Validated Peptides</option> 19 <option value="Validated_Peptides">#Validated Peptides</option>
20 <option value="Peptides">#Peptides</option> 20 <option value="Peptides">#Peptides</option>
21 <option value="Unique">#Unique</option> 21 <option value="Unique">#Unique</option>
22 <option value="Validated_PSMs">#Validated PSMs</option> 22 <option value="Validated_PSMs">#Validated PSMs</option>
23 <option value="PSMs">#PSMs</option> 23 <option value="PSMs">#PSMs</option>
66 <param name="input" value="fa_gc_content_input.fa"/> 66 <param name="input" value="fa_gc_content_input.fa"/>
67 <output name="out_file1" file="fa_gc_content_output.txt"/> 67 <output name="out_file1" file="fa_gc_content_output.txt"/>
68 </test> 68 </test>
69 </tests> 69 </tests>
70 <help> 70 <help>
71 Pre-Processing
72 ^^^^^^^^^^^^^^
73
74 This tool will read in a Peptideshaker *Report* file (tab-delimited
75 txt file) and process them to generate
76 a *Bait File, Prey File,* and *Inter File* for SAINTexpress analysis.
77
78 --------------
79
80 **Note:** The baits in the baitfile for this version need to be in
81 the same order as the files selected.
82
83
84 **1) Peptideshaker File Inputs**
85
86 Select the corresponding *Report* here.
87
88
89 **2) Select Report File Value for Quantification**
90
91 Select the column that should be used in calculating SAINT scores.
92
93 **3) Create Prey File**
94
95 Select whether or not you would like APOSTL to generate a prey file.
96
97 When making a prey file, APOSTL queries a user provided FASTA database
98 (see below) in order to extract protein amino acid lengths and gene
99 names. This may take several minutes depending on your computer and if
100 your Galaxy distribution is cluster enabled. Some users may want to run
101 SAINTexpress using the same data set while changing which baits are
102 considered test or control. It is useful to toggle **Create Prey File**
103 off in order to save time by circumventing this step as the same prey
104 file can be used for both SAINTexpress runs.
105
106 **4) Provide Uniprot FASTA database**
107
108 Please specify a FASTA file containing the protein sequence. You can
109 download the latest release of Uniprot's reviewed sequences (Swiss-Prot)
110 http://www.uniprot.org/downloads. For computing efficiency,
111 please limit your FASTA file to your species of interest. It is
112 generally advised to use the same FASTA database that was used for your
113 database searches during peptide and protein ID.
114
115 **5) Are You Providing Your Own Bait File?**
116
117 Users have two options for providing a *Bait* file. If you would like to
118 create your own *Bait* file, select Yes and designate the file below. If
119 you would like to use the **Bait Create** tool to create a *Bait* file
120 within Galaxy, please select No and proceed to the **Bait Create** tool.
121
122 **6) Bait File**
123
124 If you selected Yes above, please specify the *Bait* file you would like
125 to provide. If you selected No above, ignore this argument and proceed
126 to the **Bait Create** tool.
127
128 **Note:** Individual bait names must match to the sample names
129 within your Scaffold or MaxQuant output exactly and must contain no
130 whitespace characters (e.g. spaces) or dashes.
131
132 **7) Bait Create**
133
134 Using the **Bait Create** tool, you can create your *bait.txt* file.
135
136 **Note:** Individual bait names must match to the sample names
137 within your Scaffold or MaxQuant output exactly and must contain no
138 whitespace characters (e.g. spaces) or dashes.
139
140 APOSTL uses this bait file to find the user's baits of interest within a
141 *Samples Report* or *peptides.txt* file and when preparing the
142 *inter.txt* file.
143
144 --------------
145
146 Once your parameters have been finalized, please press the Execute
147 button to start processing. This may take a few minutes. Once your
148 process has been completed, you will see your *Bait File, Prey File,*
149 and *Inter File* on the right hand side of your panel highlighted in
150 green.
71 </help> 151 </help>
72 </tool> 152 </tool>