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"planemo upload commit 47d779aa1de5153673ac8bb1e37c9730210cbb5d"
author galaxyp
date Sat, 12 Jun 2021 18:06:28 +0000
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1 <?xml version="1.0"?>
2 <tool id="proteore_venn_diagram" name="Venn diagram" version="2021.06.08" profile="20.01">
3 <description>with JVenn</description>
4 <requirements>
5 <requirement type="package" version="3.9">python</requirement>
6 </requirements>
7 <command detect_errors="aggressive"><![CDATA[
8 python '$__tool_directory__/venn_diagram.py'
9
10 #for $i, $s in enumerate($series)
11 --input
12 #if $s.se.input == "file"
13 '$s.se.file' '$s.name' 'file' '$s.se.header' '$s.se.ncol'
14 #else
15 '$s.se.list' '$s.name' 'list'
16 #end if
17 #end for
18 --summary '$output_summary'
19 ]]></command>
20 <inputs>
21 <repeat name="series" title="List to compare" min="2" max="6">
22 <conditional name="se" >
23 <param type="select" name="input" label="Enter your list" help="Copy/paste or from a file (e.g. table)" >
24 <option value="list">Copy/paste list </option>
25 <option value="file" selected="true">Input file containing your list</option>
26 </param>
27 <when value="file">
28 <param type="data" name="file" format="txt,tabular" label="Select your file" />
29 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does file contain header?" />
30 <param type="text" name="ncol" value="c1" label="Column number on which apply the comparison" help ='For example, fill in "c1" if you want to filter the first column'>
31 <validator type="regex" message="Please enter a column number, for example: 'c1' for the first column">[c]{0,1}[0-9]+</validator>
32 </param>
33 </when>
34 <when value="list">
35 <param type="text" name="list" label="Copy/paste list" help='IDs must be separated by spaces into the form field, for example: P31946 P62258' >
36 <sanitizer>
37 <valid initial="string.printable">
38 <remove value="&apos;"/>
39 <remove value="/"/>
40 </valid>
41 <mapping initial="none">
42 <add source="&apos;" target="__sq__"/>
43 </mapping>
44 </sanitizer>
45 </param>
46 </when>
47 </conditional>
48 <param type="text" name="name" value="" label="Enter the name of this list" help="This name will be displayed on venn diagram" optional="false">
49 <sanitizer>
50 <valid initial="string.printable">
51 <remove value="&apos;"/>
52 </valid>
53 <mapping initial="none">
54 <add source="&apos;" target="__sq__"/>
55 </mapping>
56 </sanitizer>
57 <validator type="regex" message="Please enter a list name">[a-zA-Z0-9._-]+</validator>
58 </param>
59 </repeat>
60 </inputs>
61 <outputs>
62 <data format="html" name="output_summary" label="Venn diagram" from_work_dir="venn_diagram_summary.html" />
63 <data format="tsv" name="output_text" label="Venn diagram text output" from_work_dir="venn_diagram_text_output.tsv" />
64 </outputs>
65 <tests>
66 <test>
67 <repeat name="series">
68 <conditional name="se">
69 <param name="input" value="file" />
70 <param name="file" value="ID_Converter_FKW_Lacombe_et_al_2017_OK.txt" />
71 <param name="header" value="true" />
72 <param name="ncol" value="c1" />
73 </conditional>
74 <param name="name" value="Lacombe" />
75 </repeat>
76 <repeat name="series">
77 <conditional name="se">
78 <param name="input" value="file" />
79 <param name="file" value="Bredberg.txt" />
80 <param name="header" value="false" />
81 <param name="ncol" value="c1" />
82 </conditional>
83 <param name="name" value="Bredberg" />
84 </repeat>
85 <repeat name="series">
86 <conditional name="se">
87 <param name="input" value="file" />
88 <param name="file" value="Mucilli.txt" />
89 <param name="header" value="false" />
90 <param name="ncol" value="c1" />
91 </conditional>
92 <param name="name" value="Mucilli" />
93 </repeat>
94 <output name="output_summary" file="Venn_diagram_html.html" />
95 <!-- <output name="output_text" file="Venn_text_output.txt" /> -->
96 </test>
97 </tests>
98 <help><![CDATA[
99
100 **Description**
101
102 This tool is used for cross-comparison purpose between several lists having a common key (e.g. IDs) and draw a venn diagram from lists/files using the Jvenn plug-in (see Authors below).
103 It also creates output text file that contain common or specific elements between query and each compared lists/files.
104
105 -----
106
107 **Input**
108
109 Can be either a list entered in a copy/paste mode or a single or multi-columns file (txt, tsv, csv, tab, output from other tools) up to six lists/files
110
111 * **List of IDs in a copy/paste mode:** IDs have to be separated by a space (e.g. AMY1A ALB IGKC CSTA IGHA1 ACTG1)
112
113 * **for example an IDs list file** in .txt format, with 1 ID per line
114
115 .. csv-table:: tab1
116 :header: "Ids"
117
118
119 "AMY1A"
120 "ALB"
121 "IGKC"
122 "CSTA"
123 "IGHA1"
124
125 If you use a file as input list, it is necessary to specify the column number on which to apply the comparison.
126
127 Ids in a line will be split by ";", so if you have this kind of input :
128
129 .. csv-table:: tab with multiple ids per line
130 :header: "Ids"
131
132 "P22531"
133 "P04792"
134 "P01834"
135 "Q96KK5"
136 "Q06830;P60709;P13646;P31949"
137 "P06702"
138 "P14923"
139 "Q13835"
140
141 All ID will be considered (i.e. Q06830,P60709,P13646 and P31949 will be split).
142
143 .. class:: warningmark
144
145 In copy/paste mode, the number of IDs considered in input is limited to 5000.
146
147 -----
148
149 **Parameter**
150
151 "Please enter the name of this list": each list or set should be named, this information will be reported in both output (see below)
152
153 -----
154
155 **Output**
156
157 Two outputs are generated:
158
159 * **Graphical file**: Venn diagram that you can either display (interactive mode) or download as an image (PNG, SVG format)
160
161 * **Venn text output file** : a text file containing specific elements or shared by lists/files.
162
163
164 ]]></help>
165 <citations>
166 <citation type="doi">doi:10.1186/1471-2105-15-293</citation>
167 <citation type="bibtex">@book{toolsProteoRE,
168 journal = {GitHub repository},
169 publisher = {GitHub},
170 title = {ProteoRE tools},
171 url = {https://github.com/galaxyproteomics/tools-galaxyp},
172 author = {Lien Nguyen, David Chistiany, Florence Combes,Christophe Caron, Valentin Loux Yves Vandenbrouck},
173 date = {2021},
174 year = {2021},
175 }</citation>
176 </citations>
177 </tool>