-
Notifications
You must be signed in to change notification settings - Fork 0
/
prop_venn.xml
75 lines (59 loc) · 2.94 KB
/
prop_venn.xml
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
<tool id="prop_venn" name="proportional venn" version="0.4">
<description> from 2-3 sets</description>
<command interpreter="python">venner.py
#if str( $twoThree['tt']) == 'three':
--files $inputFile1,$inputFile2,$twoThree.inputFile3
--columns $column1,$column2,$twoThree.column3
--asNames $asName1,$asName2,$twoThree.asName3
#else:
--file $inputFile1,$inputFile2
--columns $column1,$column2
--asNames $asName1,$asName2
#end if
--title '$title'
--size $size
--outname $outPath
</command>
<inputs>
<param name="title" label="title" type="text" help="title of plot" optional="true" value=""/>
<param name="name" label="name" type="text" help="name of output file" value="venn of NA"/>
<param name="size" label="size" type="integer" help="size of plot ( < 540)" optional="true" value="300"/>
<param format="tabular" name="inputFile1" label="input file 1" type="data" help="tabular input file" optional="false"/>
<param name="column1" label="column index" type="integer" help="0 based index of element column" optional="false" value="0"/>
<param name="asName1" label="as name" type="text" help="nice name for columns on plot" optional="false" value="A"/>
<param format="tabular2" name="inputFile2" label="input file 2" type="data" help="tabular input file" optional="false"/>
<param name="column2" label="column index file 2" type="integer" help="0 based index of element column" optional="false" value="0"/>
<param name="asName2" label="as name file 2" type="text" help="nice name for columns on plot" optional="false" value="B"/>
<conditional name="twoThree">
<param name="tt" type="select" label="two or three">
<option value="two" selected="true">two</option>
<option value="three">three</option>
</param>
<when value="two">
</when>
<when value="three">
<param format="tabular" name="inputFile3" label="input file 3" type="data" help="tabular input file" optional="false"/>
<param name="column3" label="column index file 3" type="integer" help="0 based index of element column" optional="false" value="0"/>
<param name="asName3" label="as name file 3" type="text" help="nice name for columns on plot" optional="false" value="C"/>
</when>
</conditional>
</inputs>
<outputs>
<data name="outPath" format="html" label="${name}"/>
</outputs>
<help>
Proportional Venn Diagram:
--------------------------
Creates a proportional Venn diagram from 2 or 3 tab delimited input files.
The 0 based column index decides which column is used for extracting the sets to compare between the files.
Multiple items with the same value per column are counted as one.
Requirements:
-------------
- 2-3 tab delimited input files.
- 0 based index of the columns to extract for each file
Outputs:
--------
- Html page with the proportional Venn diagram and a table for the counts in each section.
Please turn to *Ido Tamir* in case of problems or suggestions for this tool.
</help>
</tool>