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comparison venn_diagram.xml @ 6:d1fd04dcb13a draft

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planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
author proteore
date Tue, 18 Dec 2018 10:06:31 -0500
parents 094cc3c46c5b
children 98b7912a9ceb
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5:6d0ecc59728f 6:d1fd04dcb13a
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="Jvenn" name="JVenn diagram" version="1.0"> 2 <tool id="Jvenn" name="Venn diagram" version="2018.12.18">
3 <description>processes lists and produces Venn diagrams 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
8 #for $i, $s in enumerate($series) 8 #for $i, $s in enumerate($series)
15 #end for 15 #end for
16 --summary "$output_summary" 16 --summary "$output_summary"
17 ]]></command> 17 ]]></command>
18 <inputs> 18 <inputs>
19 <!-- Files --> 19 <!-- Files -->
20 <repeat name="series" title="Lists to compare" min="2" max="6" > 20 <repeat name="series" title="List to compare" min="2" max="6" >
21 <conditional name="se" > 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)" > 22 <param type="select" name="input" label="Enter your list" help="Copy/paste or from a file (e.g. table)" >
23 <option value="list">Copy/paste your identifiers </option> 23 <option value="list">Copy/paste list </option>
24 <option value="file" selected="true">Input file containing your identifiers</option> 24 <option value="file" selected="true">Input file containing your list</option>
25 </param> 25 </param>
26 <when value="file"> 26 <when value="file">
27 <param type="data" name="file" format="txt,tabular" label="Choose a file that contains your list of IDs" /> 27 <param type="data" name="file" format="txt,tabular" label="Select your file" />
28 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does your input file contain header?" /> 28 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does file contain header?" />
29 <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' /> 29 <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' />
30 <param type="text" name="name" value="" label="Please enter the name of this list" help="This name will be displayed on venn diagram" /> 30 <param type="text" name="name" value="" label="Enter the name of this list" help="This name will be displayed on venn diagram" />
31 </when> 31 </when>
32 <when value="list"> 32 <when value="list">
33 <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' > 33 <param type="text" name="list" label="Copy/paste list" help='IDs must be separated by spaces into the form field, for example: P31946 P62258' >
34 <sanitizer> 34 <sanitizer>
35 <valid initial="string.printable"> 35 <valid initial="string.printable">
36 <remove value="&apos;"/> 36 <remove value="&apos;"/>
37 </valid> 37 </valid>
38 <mapping initial="none"> 38 <mapping initial="none">
39 <add source="&apos;" target="__sq__"/> 39 <add source="&apos;" target="__sq__"/>
40 </mapping> 40 </mapping>
41 </sanitizer> 41 </sanitizer>
42 </param> 42 </param>
43 <param type="text" name="name" value="" label="Please enter the name of this list" help="This name will be displayed on venn diagram" /> 43 <param type="text" name="name" value="" label="Enter the name of this list" help="This name will be displayed on venn diagram" />
44 </when> 44 </when>
45 </conditional> 45 </conditional>
46 </repeat> 46 </repeat>
47 </inputs> 47 </inputs>
48 <outputs> 48 <outputs>
49 <data format="html" name="output_summary" label="Venn diagram" from_work_dir="venn_diagram_summary.html" /> 49 <data format="html" name="output_summary" label="Venn diagram" from_work_dir="venn_diagram_summary.html" />
50 <data format="tabular" name="output_text" label="Venn diagram text output" from_work_dir="venn_diagram_text_output.txt" /> 50 <data format="tsv" name="output_text" label="Venn diagram text output" from_work_dir="venn_diagram_text_output.tsv" />
51 </outputs> 51 </outputs>
52 <tests> 52 <tests>
53 <test> 53 <test>
54 <repeat name="series"> 54 <repeat name="series">
55 <conditional name="se"> 55 <conditional name="se">
80 </repeat> 80 </repeat>
81 <output name="output_summary" file="Venn_diagram_html.html" /> 81 <output name="output_summary" file="Venn_diagram_html.html" />
82 <output name="output_text" file="Venn_text_output.txt" /> 82 <output name="output_text" file="Venn_text_output.txt" />
83 </test> 83 </test>
84 </tests> 84 </tests>
85 <help> 85 <help><![CDATA[
86 86
87 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. 87 **Description**
88
89 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).
90 It also creates output text file that contain common or specific elements between query and each compared lists/files.
91
92 -----
88 93
89 **Inputs** 94 **Inputs**
90 95
91 * **Query file:** A file containing different information of proteins, could be output of previous components. 96 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
92 97
93 * **File of a list of IDs:** .TXT format, each line contains 1 ID 98 * **List of IDs in a copy/paste mode:** IDs have to be separated by a space (e.g. AMY1A ALB IGKC CSTA IGHA1 ACTG1)
99
100 * **for example an IDs list file** in .txt format, with 1 ID per line
94 101
95 AMY1A 102 AMY1A
103
104 ALB
96 105
97 ALB 106 IGKC
98 107
99 IGKC 108 CSTA
100 109
101 CSTA 110 IGHA1
111
112 If you use a file as input list, it is necessary to specify the column number on which to apply the comparison.
102 113
103 IGHA1 114 -----
104 115
105 ACTG1 116 **Parameter**
106 117
107 * **List of IDs:** IDs separated by a space 118 "Please enter the name of this list": each list or set should be named, this information will be reported in both output (see below)
108 119
109 AMY1A ALB IGKC CSTA IGHA1 ACTG1 120 -----
110 121
111 If you choose a file, it is necessary to specify the column where you would like to perform the comparison. 122 **Output**
112 123
113 **Outputs** 124 Two outputs are generated:
125
126 * **Graphical file**: Venn diagram that you can either display (interactive mode) or download as image (PNG, SVG format)
127
128 * **Venn text output file** : a text file containing specific elements or shared by lists/files.
114 129
115 * **Summary file** (venn_diagram_summary.html):
116 Venn diagram: Could be downloaded as image (PNG, SVG)
117
118 * **Venn text output file**
119 A text file containing common/specific elements among compared lists/files.
120
121 ----- 130 -----
122 131
123 .. class:: infomark 132 .. class:: infomark
124 133
125 **Authors** 134 **Authors**
133 T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR 142 T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR
134 143
135 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit,Migale Bioinformatics platform 144 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit,Migale Bioinformatics platform
136 145
137 Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool. 146 Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool.
138 147 ]]></help>
139 </help> 148 <citations>
140 <citations> 149 </citations>
141 </citations>
142 </tool> 150 </tool>