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comparison SAINT_preprocessing.xml @ 21:d9592cc1df99 draft

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author bornea
date Sat, 16 Apr 2016 16:28:07 -0400
parents 0ac97a6298c2
children d3bb9de6913b
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20:0ac97a6298c2 21:d9592cc1df99
69 <param name="input" value="fa_gc_content_input.fa"/> 69 <param name="input" value="fa_gc_content_input.fa"/>
70 <output name="out_file1" file="fa_gc_content_output.txt"/> 70 <output name="out_file1" file="fa_gc_content_output.txt"/>
71 </test> 71 </test>
72 </tests> 72 </tests>
73 <help> 73 <help>
74 # Pre-Processing 74 Pre-Processing
75 ==============
75 76
76 * * * 77 --------------
77 78
78 This tool will read in a Scaffold _Samples Report_ file (tab-delimited txt file) or a MaxQuant _peptides.txt_ file and process them to generate a _Bait File, Prey File,_ and _Inter File_ for SAINTexpress analysis. 79 This tool will read in a Scaffold *Samples Report* file (tab-delimited
80 txt file) or a MaxQuant *peptides.txt* file and process them to generate
81 a *Bait File, Prey File,* and *Inter File* for SAINTexpress analysis.
79 82
80 #### 1) MaxQuant or Scaffold 83 1) MaxQuant or Scaffold
84 ^^^^^^^^^^^^^^^^^^^^^^^
81 85
82 APOSTL is able to recognize either a Scaffold _Samples Report_ file (tab-delimited txt file) or the _peptides.txt_ file output in the MaxQuant _txt_ output folder. No modifications should be made to these files. Please designate which one is being provided. 86 APOSTL is able to recognize either a Scaffold *Samples Report* file
87 (tab-delimited txt file) or the *peptides.txt* file output in the
88 MaxQuant *txt* output folder. No modifications should be made to these
89 files. Please designate which one is being provided.
83 90
84 #### 2) Scaffold or MaxQuant File Input 91 2) Scaffold or MaxQuant File Input
92 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
85 93
86 Select the corresponding _Samples Report_ or _peptides.txt_ here. 94 Select the corresponding *Samples Report* or *peptides.txt* here.
87 95
88 #### 3) Create Prey File 96 3) Create Prey File
97 ^^^^^^^^^^^^^^^^^^^
89 98
90 Select whether or not you would like APOSTL to generate a prey file. 99 Select whether or not you would like APOSTL to generate a prey file.
91 100
92 When making a prey file, APOSTL queries a user provided FASTA database (see below) in order to extract protein amino acid lengths and gene names. This may take several minutes depending on your computer and if your Galaxy distribution is cluster enabled. Some users may want to run SAINTexpress using the same data set while changing which baits are considered test or control. It is useful to toggle **Create Prey File** off in order to save time by circumventing this step as the same prey file can be used for both SAINTexpress runs. 101 When making a prey file, APOSTL queries a user provided FASTA database
102 (see below) in order to extract protein amino acid lengths and gene
103 names. This may take several minutes depending on your computer and if
104 your Galaxy distribution is cluster enabled. Some users may want to run
105 SAINTexpress using the same data set while changing which baits are
106 considered test or control. It is useful to toggle **Create Prey File**
107 off in order to save time by circumventing this step as the same prey
108 file can be used for both SAINTexpress runs.
93 109
94 #### 4) Provide Uniprot FASTA database 110 4) Provide Uniprot FASTA database
111 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
95 112
96 Please specify a FASTA file containing the protein sequence. You can download the latest release of Uniprot's reviewed sequences (Swiss-Prot) [here](http://www.uniprot.org/downloads). For computing efficiency, please limit your FASTA file to your species of interest. It is generally advised to use the same FASTA database that was used for your database searches during peptide and protein ID. 113 Please specify a FASTA file containing the protein sequence. You can
114 download the latest release of Uniprot's reviewed sequences (Swiss-Prot)
115 `here <http://www.uniprot.org/downloads>`__. For computing efficiency,
116 please limit your FASTA file to your species of interest. It is
117 generally advised to use the same FASTA database that was used for your
118 database searches during peptide and protein ID.
97 119
98 #### 5) Are You Providing Your Own Bait File? 120 5) Are You Providing Your Own Bait File?
121 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
99 122
100 Users have two options for providing a _Bait_ file. If you would like to create your own _Bait_ file, select <kbd>Yes</kbd> and designate the file below. If you would like to use the **Bait Create** tool to create a _Bait_ file within Galaxy, please select <kbd>No</kbd> and proceed to the **Bait Create** tool. 123 Users have two options for providing a *Bait* file. If you would like to
124 create your own *Bait* file, select Yes and designate the file below. If
125 you would like to use the **Bait Create** tool to create a *Bait* file
126 within Galaxy, please select No and proceed to the **Bait Create** tool.
101 127
102 #### 6) Bait File 128 6) Bait File
129 ^^^^^^^^^^^^
103 130
104 If you selected <kbd>Yes</kbd> above, please specify the _Bait_ file you would like to provide. If you selected <kbd>No</kbd> above, ignore this argument and proceed to the **Bait Create** tool. 131 If you selected Yes above, please specify the *Bait* file you would like
132 to provide. If you selected No above, ignore this argument and proceed
133 to the **Bait Create** tool.
105 134
106 > **Note:** Individual bait names must match to the sample names within your Scaffold or MaxQuant output exactly and must contain no whitespace characters (e.g. spaces) or dashes. 135 **Note:** Individual bait names must match to the sample names
136 within your Scaffold or MaxQuant output exactly and must contain no
137 whitespace characters (e.g. spaces) or dashes.
107 138
108 #### 7) Bait Create 139 7) Bait Create
140 ^^^^^^^^^^^^^^
109 141
110 Using the **Bait Create** tool, you can create your _bait.txt_ file. 142 Using the **Bait Create** tool, you can create your *bait.txt* file.
111 143
112 > **Note:** Individual bait names must match to the sample names within your Scaffold or MaxQuant output exactly and must contain no whitespace characters (e.g. spaces) or dashes. 144 **Note:** Individual bait names must match to the sample names
145 within your Scaffold or MaxQuant output exactly and must contain no
146 whitespace characters (e.g. spaces) or dashes.
113 147
114 APOSTL uses this bait file to find the user's baits of interest within a _Samples Report_ or _peptides.txt_ file and when preparing the _inter.txt_ file. 148 APOSTL uses this bait file to find the user's baits of interest within a
149 *Samples Report* or *peptides.txt* file and when preparing the
150 *inter.txt* file.
115 151
116 * * * 152 --------------
117 153
118 Once your parameters have been finalized, please press the <kbd>Execute</kbd> button to start processing. This may take a few minutes. Once your process has been completed, you will see your _Bait File, Prey File,_ and _Inter File_ on the right hand side of your panel highlighted in green. 154 Once your parameters have been finalized, please press the Execute
155 button to start processing. This may take a few minutes. Once your
156 process has been completed, you will see your *Bait File, Prey File,*
157 and *Inter File* on the right hand side of your panel highlighted in
158 green.
119 </help> 159 </help>
120 </tool> 160 </tool>