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

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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
comparison
equal deleted inserted replaced
2:c96bef0643dc 3:6aae6bc0802d
1 <tool id="venn_list" name="Venn Diagram" version="0.0.3"> 1 <tool id="venn_list" name="Venn Diagram" version="0.0.6">
2 <description>from lists</description> 2 <description>from lists</description>
3 <requirements>
4 <requirement type="python-module">rpy</requirement>
5 <requirement type="python-module">Bio</requirement>
6 </requirements>
3 <command interpreter="python"> 7 <command interpreter="python">
4 venn_list.py 8 venn_list.py
5 #if $universe.type_select=="implicit": 9 #if $universe.type_select=="implicit":
6 - - 10 - -
7 #else: 11 #else:
10 "$main_lab" 14 "$main_lab"
11 #for $s in $sets: 15 #for $s in $sets:
12 $s.set $s.set.ext "$s.lab" 16 $s.set $s.set.ext "$s.lab"
13 #end for 17 #end for
14 $PDF</command> 18 $PDF</command>
19 <stdio>
20 <!-- Anything other than zero is an error -->
21 <exit_code range="1:" />
22 <exit_code range=":-1" />
23 </stdio>
15 <inputs> 24 <inputs>
16 <param name="main_lab" size="30" type="text" value="Venn Diagram" label="Plot title"/> 25 <param name="main_lab" size="30" type="text" value="Venn Diagram" label="Plot title"/>
17 <conditional name="universe"> 26 <conditional name="universe">
18 <param name="type_select" type="select" label="Implicit or explicit full ID list?"> 27 <param name="type_select" type="select" label="Implicit or explicit full ID list?">
19 <option value="explicit">Explicit</option> 28 <option value="explicit">Explicit</option>
30 </repeat> 39 </repeat>
31 </inputs> 40 </inputs>
32 <outputs> 41 <outputs>
33 <data format="pdf" name="PDF" /> 42 <data format="pdf" name="PDF" />
34 </outputs> 43 </outputs>
35 <requirements>
36 <requirement type="python-module">rpy</requirement>
37 <requirement type="python-module">Bio</requirement>
38 </requirements>
39 <tests> 44 <tests>
40 <!-- Doesn't seem to work properly, manages to get two sets, both 45 <!-- Doesn't seem to work properly, manages to get two sets, both
41 with same FASTA file, but second with default "Group" label. 46 with same FASTA file, but second with default "Group" label. -->
42 <test> 47 <test>
43 <param name="type_select" value="explicit"/> 48 <param name="type_select" value="explicit"/>
44 <param name="main" value="venn_list.tabular" ftype="tabular"/> 49 <param name="main" value="venn_list.tabular" ftype="tabular"/>
45 <param name="main_lab" value="Some Proteins"/> 50 <param name="main_lab" value="Some Proteins"/>
46 <param name="set" value="rhodopsin_proteins.fasta"/> 51 <param name="set" value="rhodopsin_proteins.fasta"/>
47 <param name="lab" value="Rhodopsins"/> 52 <param name="lab" value="Rhodopsins"/>
48 <output name="PDF" file="venn_list1.pdf" ftype="pdf"/> 53 <output name="PDF" file="venn_list1.pdf" ftype="pdf"/>
49 </test> 54 </test>
50 -->
51 <!-- Can't use more than one repeat value in tests (yet) 55 <!-- Can't use more than one repeat value in tests (yet)
52 <test> 56 <test>
53 <param name="type_select" value="explicit"/> 57 <param name="type_select" value="explicit"/>
54 <param name="main" value="venn_list.tabular" ftype="tabular"/> 58 <param name="main" value="venn_list.tabular" ftype="tabular"/>
55 <param name="main_lab" value="Some Proteins"/> 59 <param name="main_lab" value="Some Proteins"/>
99 The Venn Diagrams are drawn using Gordon Smyth's limma package from 103 The Venn Diagrams are drawn using Gordon Smyth's limma package from
100 R/Bioconductor, http://www.bioconductor.org/ 104 R/Bioconductor, http://www.bioconductor.org/
101 105
102 The R library is called from Python via rpy, http://rpy.sourceforge.net/ 106 The R library is called from Python via rpy, http://rpy.sourceforge.net/
103 107
104 This tool uses Biopython to read SFF files. If you use this tool with 108 If you use this Galaxy tool in work leading to a scientific publication please
105 SFF files in scientific work leading to a publication, please cite the 109 cite:
106 Biopython application note: 110
111 Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013).
112 Galaxy tools and workflows for sequence analysis with applications
113 in molecular plant pathology. PeerJ 1:e167
114 http://dx.doi.org/10.7717/peerj.167
115
116 This tool uses Biopython to read and write SFF files, so you may also wish to
117 cite the Biopython application note (and Galaxy too of course):
107 118
108 Cock et al 2009. Biopython: freely available Python tools for computational 119 Cock et al 2009. Biopython: freely available Python tools for computational
109 molecular biology and bioinformatics. Bioinformatics 25(11) 1422-3. 120 molecular biology and bioinformatics. Bioinformatics 25(11) 1422-3.
110 http://dx.doi.org/10.1093/bioinformatics/btp163 pmid:19304878. 121 http://dx.doi.org/10.1093/bioinformatics/btp163 pmid:19304878.
111 122