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comparison venn_diagram.xml @ 8:bca31ac678f1 draft

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planemo upload commit 4ba1ebe7b3f5e3fabf78b5fed7ed0b92e2cbf9e5-dirty
author proteore
date Fri, 28 Jun 2019 05:18:44 -0400
parents 98b7912a9ceb
children 72295909dccf
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7:98b7912a9ceb 8:bca31ac678f1
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="Jvenn" name="Venn diagram" version="2019.02.21"> 2 <tool id="Jvenn" name="Venn diagram" version="2019.06.27">
3 <description>[JVenn] 3 <description>[JVenn]
4 </description> 4 </description>
5 <command><![CDATA[ 5 <command><![CDATA[
6 python $__tool_directory__/venn_diagram.py 6 python $__tool_directory__/venn_diagram.py
7 7
42 </mapping> 42 </mapping>
43 </sanitizer> 43 </sanitizer>
44 </param> 44 </param>
45 </when> 45 </when>
46 </conditional> 46 </conditional>
47 <param type="text" name="name" value="" label="Enter the name of this list" help="This name will be displayed on venn diagram"> 47 <param type="text" name="name" value="" label="Enter the name of this list" help="This name will be displayed on venn diagram" optional="false">
48 <sanitizer> 48 <sanitizer>
49 <valid initial="string.printable"> 49 <valid initial="string.printable">
50 <remove value="&apos;"/> 50 <remove value="&apos;"/>
51 </valid> 51 </valid>
52 <mapping initial="none"> 52 <mapping initial="none">
53 <add source="&apos;" target="__sq__"/> 53 <add source="&apos;" target="__sq__"/>
54 </mapping> 54 </mapping>
55 </sanitizer> 55 </sanitizer>
56 <validator type="regex" message="Please enter a list name">[a-zA-Z0-9._-]+</validator>
56 </param> 57 </param>
57 </repeat> 58 </repeat>
58 </inputs> 59 </inputs>
59 <outputs> 60 <outputs>
60 <data format="html" name="output_summary" label="Venn diagram" from_work_dir="venn_diagram_summary.html" /> 61 <data format="html" name="output_summary" label="Venn diagram" from_work_dir="venn_diagram_summary.html" />
100 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). 101 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).
101 It also creates output text file that contain common or specific elements between query and each compared lists/files. 102 It also creates output text file that contain common or specific elements between query and each compared lists/files.
102 103
103 ----- 104 -----
104 105
105 **Inputs** 106 **Input**
106 107
107 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 108 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
108 109
109 * **List of IDs in a copy/paste mode:** IDs have to be separated by a space (e.g. AMY1A ALB IGKC CSTA IGHA1 ACTG1) 110 * **List of IDs in a copy/paste mode:** IDs have to be separated by a space (e.g. AMY1A ALB IGKC CSTA IGHA1 ACTG1)
110 111
111 * **for example an IDs list file** in .txt format, with 1 ID per line 112 * **for example an IDs list file** in .txt format, with 1 ID per line
112 113
113 AMY1A 114 .. csv-table:: tab1
114 115 :header: "Ids"
115 ALB
116 116
117 IGKC
118 117
119 CSTA 118 "AMY1A"
120 119 "ALB"
121 IGHA1 120 "IGKC"
121 "CSTA"
122 "IGHA1"
122 123
123 If you use a file as input list, it is necessary to specify the column number on which to apply the comparison. 124 If you use a file as input list, it is necessary to specify the column number on which to apply the comparison.
125
126 Ids in a line will be split by ";", so if you have this kind of input :
127
128 .. csv-table:: tab with multiple ids per line
129 :header: "Ids"
130
131 "P22531"
132 "P04792"
133 "P01834"
134 "Q96KK5"
135 "Q06830;P60709;P13646;P31949"
136 "P06702"
137 "P14923"
138 "Q13835"
139
140 All ID will be considered (i.e. Q06830,P60709,P13646 and P31949 will be split).
141
142 .. class:: warningmark
143
144 In copy/paste mode, the number of IDs considered in input is limited to 5000.
124 145
125 ----- 146 -----
126 147
127 **Parameter** 148 **Parameter**
128 149
132 153
133 **Output** 154 **Output**
134 155
135 Two outputs are generated: 156 Two outputs are generated:
136 157
137 * **Graphical file**: Venn diagram that you can either display (interactive mode) or download as image (PNG, SVG format) 158 * **Graphical file**: Venn diagram that you can either display (interactive mode) or download as an image (PNG, SVG format)
138 159
139 * **Venn text output file** : a text file containing specific elements or shared by lists/files. 160 * **Venn text output file** : a text file containing specific elements or shared by lists/files.
140 161
141 ----- 162 -----
142 163
148 169
149 .. class:: infomark 170 .. class:: infomark
150 171
151 **Galaxy integration** 172 **Galaxy integration**
152 173
153 T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR 174 Lien Nguyen, David Chistiany, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR
154 175
155 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit,Migale Bioinformatics platform 176 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit,Migale Bioinformatics platform
156 177
157 Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool. 178 Help: contact@proteore.org for any questions or concerns about this tool.
158 ]]></help> 179 ]]></help>
159 <citations> 180 <citations>
160 </citations> 181 </citations>
161 </tool> 182 </tool>