Mercurial > repos > peterjc > venn_list
comparison tools/venn_list/venn_list.xml @ 4:991342eca214 draft
Uploaded v0.0.8a, declare Biopython dependency via Tool Shed
author | peterjc |
---|---|
date | Wed, 29 Apr 2015 11:00:41 -0400 |
parents | |
children | 26e35d5133a1 |
comparison
equal
deleted
inserted
replaced
3:6aae6bc0802d | 4:991342eca214 |
---|---|
1 <tool id="venn_list" name="Venn Diagram" version="0.0.8"> | |
2 <description>from lists</description> | |
3 <requirements> | |
4 <requirement type="python-module">rpy</requirement> | |
5 <requirement type="package" version="1.65">biopython</requirement> | |
6 <requirement type="python-module">Bio</requirement> | |
7 </requirements> | |
8 <stdio> | |
9 <!-- Anything other than zero is an error --> | |
10 <exit_code range="1:" /> | |
11 <exit_code range=":-1" /> | |
12 </stdio> | |
13 <command interpreter="python"> | |
14 venn_list.py | |
15 #if $universe.type_select=="implicit": | |
16 - - | |
17 #else: | |
18 "$main" $main.ext | |
19 #end if | |
20 "$main_lab" | |
21 #for $s in $sets: | |
22 "$s.set" $s.set.ext "$s.lab" | |
23 #end for | |
24 $PDF | |
25 </command> | |
26 <inputs> | |
27 <param name="main_lab" size="30" type="text" value="Venn Diagram" label="Plot title"/> | |
28 <conditional name="universe"> | |
29 <param name="type_select" type="select" label="Implicit or explicit full ID list?"> | |
30 <option value="explicit">Explicit</option> | |
31 <option value="implicit">Implicit (use union of sets below)</option> | |
32 </param> | |
33 <when value="explicit"> | |
34 <param name="main" type="data" format="tabular,fasta,fastq,sff" label="Full dataset (with all identifiers)" help="Tabular file (uses column one), FASTA, FASTQ or SFF file."/> | |
35 </when> | |
36 <when value="implicit"/> | |
37 </conditional> | |
38 <repeat name="sets" min="1" max="3" title="Sets"> | |
39 <param name="set" type="data" format="tabular,fasta,fastq,sff" label="Members of set" help="Tabular file (uses column one), FASTA, FASTQ or SFF file."/> | |
40 <param name="lab" size="30" type="text" value="Group" label="Caption for set"/> | |
41 </repeat> | |
42 </inputs> | |
43 <outputs> | |
44 <data format="pdf" name="PDF" /> | |
45 </outputs> | |
46 <tests> | |
47 <!-- Doesn't seem to work properly, manages to get two sets, both | |
48 with same FASTA file, but second with default "Group" label. --> | |
49 <test> | |
50 <param name="type_select" value="explicit"/> | |
51 <param name="main" value="venn_list.tabular" ftype="tabular"/> | |
52 <param name="main_lab" value="Some Proteins"/> | |
53 <param name="set" value="rhodopsin_proteins.fasta"/> | |
54 <param name="lab" value="Rhodopsins"/> | |
55 <output name="PDF" file="magic.pdf" ftype="pdf" compare="contains" /> | |
56 </test> | |
57 <!-- Can't use more than one repeat value in tests (yet) | |
58 <test> | |
59 <param name="type_select" value="explicit"/> | |
60 <param name="main" value="venn_list.tabular" ftype="tabular"/> | |
61 <param name="main_lab" value="Some Proteins"/> | |
62 <param name="count" value="3"/> | |
63 <param name="set" value="rhodopsin_proteins.fasta"/> | |
64 <param name="lab" value="Rhodopsins"/> | |
65 <param name="set" value="four_human_proteins.fasta"/> | |
66 <param name="lab" value="Human"/> | |
67 <param name="set" value="blastp_four_human_vs_rhodopsin.tabular"/> | |
68 <param name="lab" value="Human vs Rhodopsin BLAST"/> | |
69 <output name="PDF" file="magic.pdf" ftype="pdf" compare="contains" /> | |
70 </test> | |
71 --> | |
72 </tests> | |
73 <help> | |
74 | |
75 .. class:: infomark | |
76 | |
77 **TIP:** If your data is in tabular files, the identifier is assumed to be in column one. | |
78 | |
79 **What it does** | |
80 | |
81 Draws Venn Diagram for one, two or three sets (as a PDF file). | |
82 | |
83 You must supply one, two or three sets of identifiers -- corresponding | |
84 to one, two or three circles on the Venn Diagram. | |
85 | |
86 In general you should also give the full list of all the identifiers | |
87 explicitly. This is used to calculate the number of identifers outside | |
88 the circles (and check the identifiers in the other files match up). | |
89 The full list can be omitted by implicitly taking the union of the | |
90 category sets. In this case, the count outside the categories (circles) | |
91 will always be zero. | |
92 | |
93 The identifiers can be taken from the first column of a tabular file | |
94 (e.g. query names in BLAST tabular output, or signal peptide predictions | |
95 after filtering, etc), or from a sequence file (FASTA, FASTQ, SFF). | |
96 | |
97 For example, you may have a set of NGS reads (as a FASTA, FASTQ or SFF | |
98 file), and the results of several different read mappings (e.g. to | |
99 different references) as tabular files (filtered to have just the mapped | |
100 reads). You could then show the different mappings (and their overlaps) | |
101 as a Venn Diagram, and the outside count would be the unmapped reads. | |
102 | |
103 **Citations** | |
104 | |
105 The Venn Diagrams are drawn using Gordon Smyth's limma package from | |
106 R/Bioconductor, http://www.bioconductor.org/ | |
107 | |
108 The R library is called from Python via rpy, http://rpy.sourceforge.net/ | |
109 | |
110 If you use this Galaxy tool in work leading to a scientific publication please | |
111 cite: | |
112 | |
113 Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013). | |
114 Galaxy tools and workflows for sequence analysis with applications | |
115 in molecular plant pathology. PeerJ 1:e167 | |
116 http://dx.doi.org/10.7717/peerj.167 | |
117 | |
118 This tool uses Biopython to read and write SFF files, so you may also wish to | |
119 cite the Biopython application note (and Galaxy too of course): | |
120 | |
121 Cock et al 2009. Biopython: freely available Python tools for computational | |
122 molecular biology and bioinformatics. Bioinformatics 25(11) 1422-3. | |
123 http://dx.doi.org/10.1093/bioinformatics/btp163 pmid:19304878. | |
124 | |
125 </help> | |
126 <citations> | |
127 <citation type="doi">10.7717/peerj.167</citation> | |
128 <citation type="doi">10.1093/bioinformatics/15.5.356</citation> | |
129 </citations> | |
130 </tool> |