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comparison Bubblebeam_For_SAINT_wrapper.xml @ 2:d3be2b91e8d4 draft

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author bornea
date Tue, 17 Nov 2015 10:57:33 -0500
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1:248cd769eecb 2:d3be2b91e8d4
1 <tool id="Bubblebeam_For_SAINT" name="Bubblebeam For SAINT">
2 <description></description>
3 <command interpreter="python">Bubblebeam_For_SAINT_wrapper.py $list_file $prey_file $crapome $color $label $cutoff $type $outfile $NSAF_zoom $SAINT_zoom $SAINT $NSAF \$INSTALL_RUN_PATH/</command>
4 <requirements>
5 <requirement type="set_environment">INSTALL_RUN_PATH</requirement>
6 </requirements>
7 <inputs>
8 <param type="select" name="type" label="MaxQuant or Scaffold">
9 <option value="MQ">MaxQuant</option>
10 <option value="SC">Scaffold</option>
11 </param>
12 <param format="txt" name="list_file" type="data" label="List File"/>
13 <param format="txt" name="prey_file" type="data" label="Prey File"/>
14 <param format="txt" name="crapome" type="data" label="Crapome File" optional="true"/>
15 <param name="color" type="select" label="Color" optional="true">
16 <option value="crapome">Crapome</option>
17 <option value="red">Red</option>
18 <option value="blue">Blue</option>
19 </param>
20 <param type="boolean" name="label" checked="true" label="Use Labels"/>
21 <param type="float" name="cutoff" label="SAINT Score Cutoff" help="Select a value between 0 and 1 written like 0.8." value="0.8"/>
22 </inputs>
23 <outputs>
24 <data format="txt" name="outfile" label="Outfile"/>
25 <data format="png" name="NSAF_zoom" label="Zoom NSAF" />
26 <data format="png" name="SAINT_zoom" label="Zoom SAINT" />
27 <data format="png" name="NSAF" label="NSAF" />
28 <data format="png" name="SAINT" label="SAINT" />
29 </outputs>
30 <stdio>
31 <regex match="error"
32 source="stdout"
33 level="fatal"
34 description="Unknown error"/>
35 </stdio>
36
37 <tests>
38 <test>
39 <param name="input" value="fa_gc_content_input.fa"/>
40 <output name="out_file1" file="fa_gc_content_output.txt"/>
41 </test>
42 </tests>
43 <help>
44 Post-processing:
45 Once SAINTexpress has been run, APOSTL is able to read the resulting "list.txt" file. Fromhere APOSTL does a number of things:
46
47 APOSTL calculates NSAF values for each prey based on the average spectra observed for each bait
48
49 OPTIONAL: APOSTL calculates the probability of a specific interaction based on prey revalence in the CRAPome
50
51 Bubble graphs are generated for each bait where:
52
53 - x axis is the natural log of the NSAF values
54
55 - y axis is the observed log2 fold change (as compared to control)
56
57 - bubble radius is proportional to the average observed spectra
58
59 OPTIONAL: bubble color corresponds to the CRAPome probability of a specific interaction in which an 80% cutoff is applied where prey with less than 80% are colored tan
60
61 APOSTL queries ConsensusPathDB for protein-protein interactions within your data and then formats the resulting network for simple cytoscape import using the "import network from file" option.
62
63 INPUTS:
64
65 List File:
66
67 - SAINTexpress generated "list.txt" file
68
69 Prey File:
70
71 - SAINT pre-processing generated "prey.txt" file used to run SAINTexpress
72
73 Crapome File:
74
75 - raw output from Crapome Workflow 1 query (http://www.crapome.org)
76
77 Color:
78
79 - Specify the color of the bubbles within the graph.
80
81 - If "crapome" is chosen and 'crapome' file is specified, bubbles will be color based on crapome specificity
82
83 Use labels:
84
85 - Adds gene name labels to bubbles within the "zoomed in" graphs
86 SAINT Score Cutoff:
87
88 - Choose Saintscore cutoff (between 0-1) to be used for filtering the "zoomed in" graphs (default = 0.8)
89
90 - Also used for filtering during the generation of the cytoscape network
91
92 Species:
93
94 - Human, mouse, or yeast
95
96 Interaction Confidence:
97
98 - Interaction confidence value (0-1) used to filter the interactions with the ConsensusPathDB database
99
100 - Suggestions:
101
102 * low: 0
103
104 * medium: 0.5
105
106 * high: 0.7
107
108 * very high: 0.9
109
110 OUTPUTS:
111
112 Bubble Graphs:
113
114 - Unfiltered Data:
115
116 * NSAF v. Log2(FoldChange)
117
118 * SAINTscore v. Log2(FoldChange)
119
120 - Filtered by SAINT Score
121
122 * NSAF v. Log2(FoldChange)
123
124 * SAINTscore v. Log2(FoldChange)
125
126 Output.txt
127 - SAINTexpress "list.txt" output with additional columns that were used during the analysis
128 </help>
129 </tool>