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comparison Bubblebeam_For_SAINT_wrapper.xml @ 24:64b822045467 draft

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author bornea
date Fri, 29 Jan 2016 09:33:45 -0500
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23:cb7223752458 24:64b822045467
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 $inc_file $exc_file $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">
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 <param format="txt" name="inc_file" type="data" label="List of Uniprot IDs to Include" optional="true"/>
23 <param format="txt" name="exc_file" type="data" label="List of Uniprot IDs to Include" optional="true"/>
24 </inputs>
25 <outputs>
26 <data format="txt" name="outfile" label="Outfile"/>
27 <data format="png" name="NSAF_zoom" label="Zoom NSAF" />
28 <data format="png" name="SAINT_zoom" label="Zoom SAINT" />
29 <data format="png" name="NSAF" label="NSAF" />
30 <data format="png" name="SAINT" label="SAINT" />
31 </outputs>
32 <stdio>
33 <regex match="Error|error"
34 source="stdout"
35 level="fatal"
36 description="Unknown error"/>
37 <regex match="Error|error"
38 source="stderr"
39 level="fatal"
40 description="Unknown error"/>
41 <regex match="Error: bad bait"
42 source="stdout"
43 level="fatal"
44 description="Error: bad bait"/>
45 </stdio>
46 <tests>
47 <test>
48 <param name="input" value="fa_gc_content_input.fa"/>
49 <output name="out_file1" file="fa_gc_content_output.txt"/>
50 </test>
51 </tests>
52 <help>
53 **Post-processing:**
54
55 Once SAINTexpress has been run, APOSTL is able to read the resulting "list.txt" file. Fromhere APOSTL does a number of things:
56
57 APOSTL calculates NSAF values for each prey based on the average spectra observed for each bait
58
59 OPTIONAL: APOSTL calculates the probability of a specific interaction based on prey revalence in the CRAPome
60
61 Bubble graphs are generated for each bait where:
62
63 * x axis is the natural log of the NSAF values
64 * y axis is the observed log2 fold change (as compared to control)
65 * bubble radius is proportional to the average observed spectra
66
67 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
68
69 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.
70
71 INPUTS:
72
73 MaxQuant or Scaffold:
74
75 Select Scaffold if using Scaffold output and MaxQunat if using pepetides.txt from MaxQuant software.
76
77 List File:
78
79 SAINTexpress generated "list.txt" file
80
81 Prey File:
82
83 SAINT pre-processing generated "prey.txt" file used to run SAINTexpress
84
85 Crapome File:
86
87 Raw output from Crapome Workflow 1 query (http://www.crapome.org)
88
89 Color:
90
91 Specify the color of the bubbles within the graph.
92
93 If "crapome" is chosen and 'crapome' file is specified, bubbles will be color based on crapome specificity
94
95 Use labels:
96
97 Adds gene name labels to bubbles within the "zoomed in" graphs
98
99 SAINT Score Cutoff:
100
101 Choose Saintscore cutoff (between 0-1) to be used for filtering the "zoomed in" graphs (default = 0.8)
102
103 Also used for filtering during the generation of the cytoscape network
104
105 Species:
106
107 Human, mouse, or yeast
108
109 Interaction Confidence:
110
111 Interaction confidence value (0-1) used to filter the interactions with the ConsensusPathDB database
112
113 Suggestions:
114
115 * low: 0
116 * medium: 0.5
117 * high: 0.7
118 * very high: 0.9
119
120 List of Uniprot IDs to Include:
121
122 Text file with one column of uniprot IDs. Only the Uniprot IDs in the file will be used on the resulting bubblebeam.
123
124 List of Uniprot IDs to Exclude:
125
126 Text file with one column of uniprot IDs. The Uniprot IDs in this list will not be used in generating the bubblebeam.
127
128 OUTPUTS:
129
130 Bubble Graphs:
131
132 Unfiltered Data:
133
134 * NSAF v. Log2(FoldChange)
135 * SAINTscore v. Log2(FoldChange)
136
137 Filtered by SAINT Score
138
139 * NSAF v. Log2(FoldChange)
140 * SAINTscore v. Log2(FoldChange)
141
142 Output.txt
143
144 SAINTexpress "list.txt" output with additional columns that were used during the analysis.
145 </help>
146 </tool>