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comparison SAINT_preprocessing.xml @ 55:340cc5988c31 draft

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author bornea
date Sat, 27 Aug 2016 21:01:12 -0400
parents 8031a47f67c6
children 5ad68d3a11cc
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54:0f5028e0c39c 55:340cc5988c31
19 ${ba.assign} 19 ${ba.assign}
20 ${ba.T_C} 20 ${ba.T_C}
21 #end for 21 #end for
22 " 22 "
23 $Bait_file \$INSTALL_RUN_PATH/ $bait_bool $bait_file_in 23 $Bait_file \$INSTALL_RUN_PATH/ $bait_bool $bait_file_in
24 #elif (str($type) == 'Peptideshaker'):
25 Protein_report_processing.py "$input" $Bait_file $use_metric $fasta_db $preybool
26 "
27 #for $ba in $bait
28 ${ba.bait1}
29 ${ba.assign}
30 ${ba.T_C}
31 #end for
32 "
33 \$INSTALL_RUN_PATH/ $bait_bool $bait_file_in $Inter_file $Prey_file
24 #end if 34 #end if
25 </command> 35 </command>
26 <requirements> 36 <requirements>
27 <requirement type="set_environment">INSTALL_RUN_PATH</requirement> 37 <requirement type="set_environment">INSTALL_RUN_PATH</requirement>
28 <requirement type="package" version="3.2.1">package_r_3_2_1</requirement>
29 </requirements> 38 </requirements>
30 <inputs> 39 <inputs>
31 <param type="select" name="type" label="MaxQuant or Scaffold"> 40 <conditional name="type_select">
32 <option value="MaxQuant">MaxQuant</option> 41 <param type="select" name="type" label="MaxQuant or Scaffold">
33 <option value="Scaffold">Scaffold</option> 42 <option value="MaxQuant">MaxQuant</option>
34 </param> 43 <option value="Scaffold">Scaffold</option>
35 <param format="dat" name="input" type="data" label="Scaffold or MaxQuant peptides Output"/> 44 <option value="Peptideshaker">Peptideshaker</option>
36 <param type="boolean" name="preybool" checked="true" label="Create Prey File"/> 45 </param>
37 <param type="data" name="fasta_db" format="fasta" label="Provide Uniprot Fasta database" optional="true"/> 46 <when value="MaxQuant">
38 <param name="bait_bool" type="boolean" checked="true" label="Are You Providing Your Own bait file?"/> 47 <param format="dat" name="input" type="data" label="MaxQuant peptides Output"/>
39 <param type="data" format="dat" name="bait_file_in" label="Bait File" optional="true"/> 48 <param type="boolean" name="preybool" checked="true" label="Create Prey File"/>
40 <repeat name="bait" title="Bait Create"> 49 <param type="data" name="fasta_db" format="fasta" label="Provide Uniprot Fasta database" optional="true"/>
41 <param name="bait1" type="text" size="100" label="Bait"/> 50 <param name="bait_bool" type="boolean" checked="true" label="Are You Providing Your Own bait file?"/>
42 <param name="assign" type="text" size="100" label="Group Assignment"/> 51 <param type="data" format="dat" name="bait_file_in" label="Bait File" optional="true"/>
43 <param name="T_C" type="boolean" checked="true" label="Is this a Control?"/> 52 <repeat name="bait" title="Bait Create">
44 </repeat> 53 <param name="bait1" type="text" size="100" label="Bait"/>
45 54 <param name="assign" type="text" size="100" label="Group Assignment"/>
55 <param name="T_C" type="boolean" checked="true" label="Is this a Control?"/>
56 </repeat>
57 <when value="Scaffold">
58 <param format="dat" name="input" type="data" label="Scaffold Output"/>
59 <param type="boolean" name="preybool" checked="true" label="Create Prey File"/>
60 <param type="data" name="fasta_db" format="fasta" label="Provide Uniprot Fasta database" optional="true"/>
61 <param name="bait_bool" type="boolean" checked="true" label="Are You Providing Your Own bait file?"/>
62 <param type="data" format="dat" name="bait_file_in" label="Bait File" optional="true"/>
63 <repeat name="bait" title="Bait Create">
64 <param name="bait1" type="text" size="100" label="Bait"/>
65 <param name="assign" type="text" size="100" label="Group Assignment"/>
66 <param name="T_C" type="boolean" checked="true" label="Is this a Control?"/>
67 </repeat>
68 </when>
69 <when value="Peptideshaker">
70 <param format="dat" name="input" type="data" label="Peptideshaker Output" multiple="true"/>
71 <param type="select" name="use_metric" label="Select Report File Value for Quantification">
72 <option value="Validated_Peptides">#Validated Peptides</option>
73 <option value="Peptides">#Peptides</option>
74 <option value="Unique">#Unique</option>
75 <option value="Validated_PSMs">#Validated PSMs</option>
76 <option value="PSMs">#PSMs</option>
77 </param>
78 <param type="boolean" name="preybool" checked="true" label="Create Prey File"/>
79 <param type="data" name="fasta_db" format="fasta" label="Provide Uniprot Fasta database" optional="true"/>
80 <param name="bait_bool" type="boolean" checked="true" label="Are You Providing Your Own bait file?"/>
81 <param type="data" format="dat" name="bait_file_in" label="Bait File" optional="true"/>
82 <repeat name="bait" title="Bait Create">
83 <param name="bait1" type="text" size="100" label="Bait"/>
84 <param name="assign" type="text" size="100" label="Group Assignment"/>
85 <param name="T_C" type="boolean" checked="true" label="Is this a Control?"/>
86 </repeat>
87 </when>
88 </conditional>
46 </inputs> 89 </inputs>
47 <outputs> 90 <outputs>
48 <data format="txt" name="Inter_file" label="Inter File"/> 91 <data format="txt" name="Inter_file" label="Inter File"/>
49 <data format="txt" name="Prey_file" label="Prey File" /> 92 <data format="txt" name="Prey_file" label="Prey File" />
50 <data format="txt" name="Bait_file" label="Bait File" /> 93 <data format="txt" name="Bait_file" label="Bait File" />
81 <help> 124 <help>
82 Pre-Processing 125 Pre-Processing
83 ^^^^^^^^^^^^^^ 126 ^^^^^^^^^^^^^^
84 127
85 This tool will read in a Scaffold *Samples Report* file (tab-delimited 128 This tool will read in a Scaffold *Samples Report* file (tab-delimited
86 txt file) or a MaxQuant *peptides.txt* file and process them to generate 129 txt file), multiple Peptideshaker *Protein Report* files or a MaxQuant
87 a *Bait File, Prey File,* and *Inter File* for SAINTexpress analysis. 130 *peptides.txt* file and process them to generate a *Bait File, Prey
131 File,* and *Inter File* for SAINTexpress analysis.
88 132
89 -------------- 133 --------------
90 134
91 **1) MaxQuant or Scaffold** 135 **1) MaxQuant or Scaffold**
92 136
135 to the **Bait Create** tool. 179 to the **Bait Create** tool.
136 180
137 **Note:** Individual bait names must match to the sample names 181 **Note:** Individual bait names must match to the sample names
138 within your Scaffold or MaxQuant output exactly and must contain no 182 within your Scaffold or MaxQuant output exactly and must contain no
139 whitespace characters (e.g. spaces) or dashes. 183 whitespace characters (e.g. spaces) or dashes.
184
185 **Note:** When using Peptideshaker output the baits in the baitfile
186 need to be in the same order as the files selected.
140 187
141 **7) Bait Create** 188 **7) Bait Create**
142 189
143 Using the **Bait Create** tool, you can create your *bait.txt* file. 190 Using the **Bait Create** tool, you can create your *bait.txt* file.
144 191