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date Sun, 26 Nov 2017 19:09:40 -0500
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1 <?xml version="1.0"?>
2 <tool id="Jvenn" name="Venn diagram" version="1.0">
3 <description>compare lists plotting Venn Diagram (based on Jvenn).
4 </description>
5 <command><![CDATA[
6 python $__tool_directory__/venn_diagram.py
7
8 #for $i, $s in enumerate($series)
9 --input
10 #if $s.se.input == "file"
11 "$s.se.file" "$s.se.name" "file" "$s.se.header" "$s.se.ncol"
12 #else
13 "$s.se.list" "$s.se.name" "list"
14 #end if
15 #end for
16 --summary "$output_summary"
17 ]]></command>
18 <inputs>
19 <!-- Files -->
20 <repeat name="series" title="Lists to compare" min="2" max="6" >
21 <conditional name="se" >
22 <param type="select" name="input" label="Please provide your identifiers" help="Copy/paste or ID list from a file (e.g. table)" >
23 <option value="list">Copy/paste your identifiers </option>
24 <option value="file">Input file containing your identifiers</option>
25
26 </param>
27 <when value="file">
28 <param type="data" name="file" format="txt,tabular" label="Choose a file that contains your list of IDs" />
29 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does your input file contain header?" />
30 <param type="text" name="ncol" value="c1" label="Please specify the column where you would like to apply the comparison" help ='For example, fill in "c1" if you want to filter the first column' />
31 <param type="text" name="name" value="" label="Please enter the name of this list" help="This name will be displayed on venn diagram" />
32 </when>
33 <when value="list">
34 <param type="text" name="list" label="Copy/paste your identifiers" help='IDs must be separated by spaces into the form field, for example: P31946 P62258' >
35 <sanitizer>
36 <valid initial="string.printable">
37 <remove value="&apos;"/>
38 </valid>
39 <mapping initial="none">
40 <add source="&apos;" target="__sq__"/>
41 </mapping>
42 </sanitizer>
43 </param>
44 <param type="text" name="name" value="" label="Please enter the name of this list" help="This name will be displayed on venn diagram" />
45 </when>
46 </conditional>
47 </repeat>
48 </inputs>
49 <outputs>
50 <data format="html" name="output_summary" label="Venn diagram" from_work_dir="venn_diagram_summary.html" />
51 <data format="tabular" name="output_text" label="Venn diagram text output" from_work_dir="venn_diagram_text_output.txt" />
52 </outputs>
53 <tests>
54 <test>
55 <repeat name="series">
56 <conditional name="se">
57 <param name="input" value="mq_file" />
58 <param name="mq_file" value="DESeq.txt" />
59 <param name="header" value="false" />
60 <param name="ncol" value="c1" />
61 <param name="name" value="DESeq" />
62 </conditional>
63 </repeat>
64 <repeat name="series">
65 <conditional name="se">
66 <param name="input" value="mq_file" />
67 <param name="mq_file" value="FQ.txt" />
68 <param name="header" value="false" />
69 <param name="ncol" value="c1" />
70 <param name="name" value="FQ" />
71 </conditional>
72 </repeat>
73 <repeat name="series">
74 <conditional name="se">
75 <param name="input" value="mq_file" />
76 <param name="mq_file" value="RPKM.txt" />
77 <param name="header" value="false" />
78 <param name="ncol" value="c1" />
79 <param name="name" value="RPKM" />
80 </conditional>
81 </repeat>
82 <repeat name="series">
83 <conditional name="se">
84 <param name="input" value="mq_file" />
85 <param name="mq_file" value="TC.txt" />
86 <param name="header" value="false" />
87 <param name="ncol" value="c1" />
88 <param name="name" value="TC" />
89 </conditional>
90 </repeat>
91 <repeat name="series">
92 <conditional name="se">
93 <param name="input" value="mq_file" />
94 <param name="mq_file" value="TMM.txt" />
95 <param name="header" value="false" />
96 <param name="ncol" value="c1" />
97 <param name="name" value="TMM" />
98 </conditional>
99 </repeat>
100 <repeat name="series">
101 <conditional name="se">
102 <param name="input" value="mq_file" />
103 <param name="mq_file" value="UQ.txt" />
104 <param name="header" value="false" />
105 <param name="ncol" value="c1" />
106 <param name="name" value="UQ" />
107 </conditional>
108 </repeat>
109 <output name="output_summary" file="venn_diagram_summary.html" />
110 <output name="output_text" file="venn_diagram_text_output.txt" />
111
112 </test>
113 </tests>
114 <help>
115
116 This tool draw a venn diagram from lists/files using Jvenn plug-in (http://jvenn.toulouse.inra.fr/app/index.html). It also creates output files that contain common or specific elements between query and each compared lists/files.
117
118 **Inputs**
119
120 * **Query file:** A file containing different information of proteins, could be output of previous components.
121
122 * **File of a list of IDs:** .TXT format, each line contains 1 ID
123
124 AMY1A
125
126 ALB
127
128 IGKC
129
130 CSTA
131
132 IGHA1
133
134 ACTG1
135
136 * **List of IDs:** IDs separated by a space
137 AMY1A ALB IGKC CSTA IGHA1 ACTG1
138
139 If you choose a file, it is necessary to specify the column where you would like to perform the comparison.
140
141 **Outputs**
142
143 * **Summary file** (venn_diagram_summary.html):
144 Venn diagram: Could be downloaded as image (PNG, SVG)
145
146 * **Venn text output file**
147 A text file containing common/specific elements among compared lists/files.
148
149 -----
150
151 .. class:: infomark
152
153 **Authors**
154
155 Philippe Bardou, Jérôme Mariette, Frédéric Escudié, Christophe Djemiel and Christophe Klopp. jvenn: an interactive Venn diagram viewer. BMC Bioinformatics 2014, 15:293 doi:10.1186/1471-2105-15-293
156
157 .. class:: infomark
158
159 **Galaxy integration**
160
161 T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR
162
163 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit,Migale Bioinformatics platform
164
165 Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool.
166
167 </help>
168 <citations>
169 </citations>
170 </tool>