Mercurial > repos > peterjc > venn_list

annotate tools/plotting/venn_list.xml @ 3:6aae6bc0802d draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded v0.0.6, basic unit test, MIT licence, RST README, citation information, development moved to GitHub
author peterjc
date Wed, 18 Sep 2013 06:19:51 -0400
parents baf7031d470e
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
3
6aae6bc0802d Uploaded v0.0.6, basic unit test, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents: 0
diff changeset
1 <tool id="venn_list" name="Venn Diagram" version="0.0.6">
0
baf7031d470e Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
2 <description>from lists</description>
3
6aae6bc0802d Uploaded v0.0.6, basic unit test, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents: 0
diff changeset
3 <requirements>
6aae6bc0802d Uploaded v0.0.6, basic unit test, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents: 0
diff changeset
4 <requirement type="python-module">rpy</requirement>
6aae6bc0802d Uploaded v0.0.6, basic unit test, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents: 0
diff changeset
5 <requirement type="python-module">Bio</requirement>
6aae6bc0802d Uploaded v0.0.6, basic unit test, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents: 0
diff changeset
6 </requirements>
0
baf7031d470e Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
7 <command interpreter="python">
baf7031d470e Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
8 venn_list.py
baf7031d470e Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
9 #if $universe.type_select=="implicit":
baf7031d470e Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
10 - -
baf7031d470e Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
11 #else:
baf7031d470e Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
12 $main $main.ext
baf7031d470e Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
13 #end if
baf7031d470e Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
14 "$main_lab"
baf7031d470e Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
15 #for $s in $sets:
baf7031d470e Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
16 $s.set $s.set.ext "$s.lab"
baf7031d470e Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
17 #end for
baf7031d470e Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
18 $PDF</command>
3
6aae6bc0802d Uploaded v0.0.6, basic unit test, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents: 0
diff changeset
19 <stdio>
6aae6bc0802d Uploaded v0.0.6, basic unit test, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents: 0
diff changeset
20 <!-- Anything other than zero is an error -->
6aae6bc0802d Uploaded v0.0.6, basic unit test, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents: 0
diff changeset
21 <exit_code range="1:" />
6aae6bc0802d Uploaded v0.0.6, basic unit test, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents: 0
diff changeset
22 <exit_code range=":-1" />
6aae6bc0802d Uploaded v0.0.6, basic unit test, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents: 0
diff changeset
23 </stdio>
0
baf7031d470e Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
24 <inputs>
baf7031d470e Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
25 <param name="main_lab" size="30" type="text" value="Venn Diagram" label="Plot title"/>
baf7031d470e Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
26 <conditional name="universe">
baf7031d470e Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
27 <param name="type_select" type="select" label="Implicit or explicit full ID list?">
baf7031d470e Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
28 <option value="explicit">Explicit</option>
baf7031d470e Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
29 <option value="implicit">Implicit (use union of sets below)</option>
baf7031d470e Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
30 </param>
baf7031d470e Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
31 <when value="explicit">
baf7031d470e Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
32 <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."/>
baf7031d470e Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
33 </when>
baf7031d470e Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
34 <when value="implicit"/>
baf7031d470e Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
35 </conditional>
baf7031d470e Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
36 <repeat name="sets" min="1" max="3" title="Sets">
baf7031d470e Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
37 <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."/>
baf7031d470e Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
38 <param name="lab" size="30" type="text" value="Group" label="Caption for set"/>
baf7031d470e Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
39 </repeat>
baf7031d470e Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
40 </inputs>
baf7031d470e Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
41 <outputs>
baf7031d470e Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
42 <data format="pdf" name="PDF" />
baf7031d470e Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
43 </outputs>
baf7031d470e Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
44 <tests>
baf7031d470e Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
45 <!-- Doesn't seem to work properly, manages to get two sets, both
3
6aae6bc0802d Uploaded v0.0.6, basic unit test, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents: 0
diff changeset
46 with same FASTA file, but second with default "Group" label. -->
0
baf7031d470e Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
47 <test>
baf7031d470e Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
48 <param name="type_select" value="explicit"/>
baf7031d470e Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
49 <param name="main" value="venn_list.tabular" ftype="tabular"/>
baf7031d470e Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
50 <param name="main_lab" value="Some Proteins"/>
baf7031d470e Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
51 <param name="set" value="rhodopsin_proteins.fasta"/>
baf7031d470e Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
52 <param name="lab" value="Rhodopsins"/>
baf7031d470e Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
53 <output name="PDF" file="venn_list1.pdf" ftype="pdf"/>
baf7031d470e Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
54 </test>
baf7031d470e Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
55 <!-- Can't use more than one repeat value in tests (yet)
baf7031d470e Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
56 <test>
baf7031d470e Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
57 <param name="type_select" value="explicit"/>
baf7031d470e Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
58 <param name="main" value="venn_list.tabular" ftype="tabular"/>
baf7031d470e Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
59 <param name="main_lab" value="Some Proteins"/>
baf7031d470e Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
60 <param name="count" value="3"/>
baf7031d470e Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
61 <param name="set" value="rhodopsin_proteins.fasta"/>
baf7031d470e Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
62 <param name="lab" value="Rhodopsins"/>
baf7031d470e Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
63 <param name="set" value="four_human_proteins.fasta"/>
baf7031d470e Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
64 <param name="lab" value="Human"/>
baf7031d470e Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
65 <param name="set" value="blastp_four_human_vs_rhodopsin.tabular"/>
baf7031d470e Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
66 <param name="lab" value="Human vs Rhodopsin BLAST"/>
baf7031d470e Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
67 <output name="PDF" file="venn_list3.pdf" ftype="pdf"/>
baf7031d470e Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
68 </test>
baf7031d470e Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
69 -->
baf7031d470e Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
70 </tests>
baf7031d470e Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
71 <help>
baf7031d470e Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
72
baf7031d470e Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
73 .. class:: infomark
baf7031d470e Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
74
baf7031d470e Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
75 **TIP:** If your data is in tabular files, the identifier is assumed to be in column one.
baf7031d470e Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
76
baf7031d470e Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
77 **What it does**
baf7031d470e Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
78
baf7031d470e Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
79 Draws Venn Diagram for one, two or three sets (as a PDF file).
baf7031d470e Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
80
baf7031d470e Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
81 You must supply one, two or three sets of identifiers -- corresponding
baf7031d470e Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
82 to one, two or three circles on the Venn Diagram.
baf7031d470e Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
83
baf7031d470e Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
84 In general you should also give the full list of all the identifiers
baf7031d470e Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
85 explicitly. This is used to calculate the number of identifers outside
baf7031d470e Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
86 the circles (and check the identifiers in the other files match up).
baf7031d470e Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
87 The full list can be omitted by implicitly taking the union of the
baf7031d470e Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
88 category sets. In this case, the count outside the categories (circles)
baf7031d470e Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
89 will always be zero.
baf7031d470e Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
90
baf7031d470e Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
91 The identifiers can be taken from the first column of a tabular file
baf7031d470e Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
92 (e.g. query names in BLAST tabular output, or signal peptide predictions
baf7031d470e Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
93 after filtering, etc), or from a sequence file (FASTA, FASTQ, SFF).
baf7031d470e Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
94
baf7031d470e Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
95 For example, you may have a set of NGS reads (as a FASTA, FASTQ or SFF
baf7031d470e Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
96 file), and the results of several different read mappings (e.g. to
baf7031d470e Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
97 different references) as tabular files (filtered to have just the mapped
baf7031d470e Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
98 reads). You could then show the different mappings (and their overlaps)
baf7031d470e Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
99 as a Venn Diagram, and the outside count would be the unmapped reads.
baf7031d470e Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
100
baf7031d470e Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
101 **Citations**
baf7031d470e Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
102
baf7031d470e Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
103 The Venn Diagrams are drawn using Gordon Smyth's limma package from
baf7031d470e Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
104 R/Bioconductor, http://www.bioconductor.org/
baf7031d470e Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
105
baf7031d470e Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
106 The R library is called from Python via rpy, http://rpy.sourceforge.net/
baf7031d470e Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
107
3
6aae6bc0802d Uploaded v0.0.6, basic unit test, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents: 0
diff changeset
108 If you use this Galaxy tool in work leading to a scientific publication please
6aae6bc0802d Uploaded v0.0.6, basic unit test, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents: 0
diff changeset
109 cite:
6aae6bc0802d Uploaded v0.0.6, basic unit test, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents: 0
diff changeset
110
6aae6bc0802d Uploaded v0.0.6, basic unit test, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents: 0
diff changeset
111 Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013).
6aae6bc0802d Uploaded v0.0.6, basic unit test, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents: 0
diff changeset
112 Galaxy tools and workflows for sequence analysis with applications
6aae6bc0802d Uploaded v0.0.6, basic unit test, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents: 0
diff changeset
113 in molecular plant pathology. PeerJ 1:e167
6aae6bc0802d Uploaded v0.0.6, basic unit test, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents: 0
diff changeset
114 http://dx.doi.org/10.7717/peerj.167
6aae6bc0802d Uploaded v0.0.6, basic unit test, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents: 0
diff changeset
115
6aae6bc0802d Uploaded v0.0.6, basic unit test, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents: 0
diff changeset
116 This tool uses Biopython to read and write SFF files, so you may also wish to
6aae6bc0802d Uploaded v0.0.6, basic unit test, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents: 0
diff changeset
117 cite the Biopython application note (and Galaxy too of course):
0
baf7031d470e Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
118
baf7031d470e Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
119 Cock et al 2009. Biopython: freely available Python tools for computational
baf7031d470e Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
120 molecular biology and bioinformatics. Bioinformatics 25(11) 1422-3.
baf7031d470e Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
121 http://dx.doi.org/10.1093/bioinformatics/btp163 pmid:19304878.
baf7031d470e Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
122
baf7031d470e Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
123 </help>
baf7031d470e Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
124 </tool>