Mercurial > repos > proteore > proteore_venn_diagram

comparison venn_diagram.xml @ 1:760470ddb9ca draft

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planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
author proteore
date Fri, 16 Feb 2018 03:37:16 -0500
parents 9d4f20618ab4
children 774d9cbe6937
comparison
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0:9d4f20618ab4 1:760470ddb9ca
20 <repeat name="series" title="Lists to compare" min="2" max="6" > 20 <repeat name="series" title="Lists 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="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> 23 <option value="list">Copy/paste your identifiers </option>
24 <option value="file">Input file containing your identifiers</option> 24 <option value="file">Input file containing your identifiers</option>
25
26 </param> 25 </param>
27 <when value="file"> 26 <when value="file">
28 <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="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?" /> 28 <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' /> 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' />
52 </outputs> 51 </outputs>
53 <tests> 52 <tests>
54 <test> 53 <test>
55 <repeat name="series"> 54 <repeat name="series">
56 <conditional name="se"> 55 <conditional name="se">
57 <param name="input" value="mq_file" /> 56 <param name="input" value="file" />
58 <param name="mq_file" value="DESeq.txt" /> 57 <param name="file" value="ID_Converter_FKW_Lacombe_et_al_2017_OK.txt" />
59 <param name="header" value="false" /> 58 <param name="header" value="true" />
60 <param name="ncol" value="c1" /> 59 <param name="ncol" value="c1" />
61 <param name="name" value="DESeq" /> 60 <param name="name" value="Lacombe" />
62 </conditional> 61 </conditional>
63 </repeat> 62 </repeat>
64 <repeat name="series"> 63 <repeat name="series">
65 <conditional name="se"> 64 <conditional name="se">
66 <param name="input" value="mq_file" /> 65 <param name="input" value="file" />
67 <param name="mq_file" value="FQ.txt" /> 66 <param name="file" value="Mucilli.txt" />
68 <param name="header" value="false" /> 67 <param name="header" value="false" />
69 <param name="ncol" value="c1" /> 68 <param name="ncol" value="c1" />
70 <param name="name" value="FQ" /> 69 <param name="name" value="Mucilli" />
71 </conditional> 70 </conditional>
72 </repeat> 71 </repeat>
73 <repeat name="series"> 72 <repeat name="series">
74 <conditional name="se"> 73 <conditional name="se">
75 <param name="input" value="mq_file" /> 74 <param name="input" value="file" />
76 <param name="mq_file" value="RPKM.txt" /> 75 <param name="file" value="Bredberg.txt" />
77 <param name="header" value="false" /> 76 <param name="header" value="false" />
78 <param name="ncol" value="c1" /> 77 <param name="ncol" value="c1" />
79 <param name="name" value="RPKM" /> 78 <param name="name" value="Bredberg" />
80 </conditional> 79 </conditional>
81 </repeat> 80 </repeat>
82 <repeat name="series"> 81 <output name="output_summary" file="Venn_diagram_html.html" />
83 <conditional name="se"> 82 <output name="output_text" file="Venn_text_output.txt" />
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> 83 </test>
113 </tests> 84 </tests>
114 <help> 85 <help>
115 86
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. 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.
118 **Inputs** 89 **Inputs**
119 90
120 * **Query file:** A file containing different information of proteins, could be output of previous components. 91 * **Query file:** A file containing different information of proteins, could be output of previous components.
121 92
122 * **File of a list of IDs:** .TXT format, each line contains 1 ID 93 * **File of a list of IDs:** .TXT format, each line contains 1 ID
123 94
124 AMY1A 95 AMY1A
125 96
126 ALB 97 ALB
127 98
128 IGKC 99 IGKC
129 100
130 CSTA 101 CSTA
131 102
132 IGHA1 103 IGHA1
133 104
134 ACTG1 105 ACTG1
135 106
136 * **List of IDs:** IDs separated by a space 107 * **List of IDs:** IDs separated by a space
137 AMY1A ALB IGKC CSTA IGHA1 ACTG1 108
109 AMY1A ALB IGKC CSTA IGHA1 ACTG1
138 110
139 If you choose a file, it is necessary to specify the column where you would like to perform the comparison. 111 If you choose a file, it is necessary to specify the column where you would like to perform the comparison.
140 112
141 **Outputs** 113 **Outputs**
142 114