Mercurial > repos > proteore > proteore_venn_diagram
comparison venn_diagram.xml @ 8:bca31ac678f1 draft
planemo upload commit 4ba1ebe7b3f5e3fabf78b5fed7ed0b92e2cbf9e5-dirty
author | proteore |
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date | Fri, 28 Jun 2019 05:18:44 -0400 |
parents | 98b7912a9ceb |
children | 72295909dccf |
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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="'"/> | 50 <remove value="'"/> |
51 </valid> | 51 </valid> |
52 <mapping initial="none"> | 52 <mapping initial="none"> |
53 <add source="'" target="__sq__"/> | 53 <add source="'" 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> |