Mercurial > repos > peterjc > venn_list

annotate tools/plotting/venn_list.xml @ 6:6ebfb498c2c4 draft

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Uploaded v0.0.6 take 3, MIT licence, RST README, citation information
author peterjc
date Wed, 11 Sep 2013 06:46:31 -0400
parents 29fcd027d67a
children 86bd05e9039b
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1 <tool id="venn_list" name="Venn Diagram" version="0.0.6">
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2 <description>from lists</description>
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3 <requirements>
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4 <requirement type="python-module">rpy</requirement>
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5 <requirement type="python-module">Bio</requirement>
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6 </requirements>
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7 <command interpreter="python">
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8 venn_list.py
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9 #if $universe.type_select=="implicit":
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10 - -
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11 #else:
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12 $main $main.ext
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13 #end if
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14 "$main_lab"
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15 #for $s in $sets:
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16 $s.set $s.set.ext "$s.lab"
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17 #end for
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18 $PDF</command>
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19 <stdio>
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20 <!-- Anything other than zero is an error -->
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21 <exit_code range="1:" />
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22 <exit_code range=":-1" />
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23 </stdio>
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24 <inputs>
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25 <param name="main_lab" size="30" type="text" value="Venn Diagram" label="Plot title"/>
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26 <conditional name="universe">
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27 <param name="type_select" type="select" label="Implicit or explicit full ID list?">
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28 <option value="explicit">Explicit</option>
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29 <option value="implicit">Implicit (use union of sets below)</option>
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30 </param>
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31 <when value="explicit">
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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."/>
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33 </when>
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34 <when value="implicit"/>
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35 </conditional>
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36 <repeat name="sets" min="1" max="3" title="Sets">
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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."/>
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38 <param name="lab" size="30" type="text" value="Group" label="Caption for set"/>
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39 </repeat>
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40 </inputs>
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41 <outputs>
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42 <data format="pdf" name="PDF" />
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43 </outputs>
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44 <tests>
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45 <!-- Doesn't seem to work properly, manages to get two sets, both
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46 with same FASTA file, but second with default "Group" label. -->
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47 <test>
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48 <param name="type_select" value="explicit"/>
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49 <param name="main" value="venn_list.tabular" ftype="tabular"/>
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50 <param name="main_lab" value="Some Proteins"/>
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51 <param name="set" value="rhodopsin_proteins.fasta"/>
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52 <param name="lab" value="Rhodopsins"/>
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53 <output name="PDF" file="venn_list1.pdf" ftype="pdf"/>
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54 </test>
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55 <!-- Can't use more than one repeat value in tests (yet)
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56 <test>
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57 <param name="type_select" value="explicit"/>
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58 <param name="main" value="venn_list.tabular" ftype="tabular"/>
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59 <param name="main_lab" value="Some Proteins"/>
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60 <param name="count" value="3"/>
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61 <param name="set" value="rhodopsin_proteins.fasta"/>
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62 <param name="lab" value="Rhodopsins"/>
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63 <param name="set" value="four_human_proteins.fasta"/>
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64 <param name="lab" value="Human"/>
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65 <param name="set" value="blastp_four_human_vs_rhodopsin.tabular"/>
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66 <param name="lab" value="Human vs Rhodopsin BLAST"/>
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67 <output name="PDF" file="venn_list3.pdf" ftype="pdf"/>
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68 </test>
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69 -->
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70 </tests>
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71 <help>
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72
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73 .. class:: infomark
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74
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75 **TIP:** If your data is in tabular files, the identifier is assumed to be in column one.
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76
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77 **What it does**
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78
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79 Draws Venn Diagram for one, two or three sets (as a PDF file).
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80
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81 You must supply one, two or three sets of identifiers -- corresponding
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82 to one, two or three circles on the Venn Diagram.
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83
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84 In general you should also give the full list of all the identifiers
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85 explicitly. This is used to calculate the number of identifers outside
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86 the circles (and check the identifiers in the other files match up).
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87 The full list can be omitted by implicitly taking the union of the
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88 category sets. In this case, the count outside the categories (circles)
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89 will always be zero.
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90
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91 The identifiers can be taken from the first column of a tabular file
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92 (e.g. query names in BLAST tabular output, or signal peptide predictions
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93 after filtering, etc), or from a sequence file (FASTA, FASTQ, SFF).
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94
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95 For example, you may have a set of NGS reads (as a FASTA, FASTQ or SFF
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96 file), and the results of several different read mappings (e.g. to
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97 different references) as tabular files (filtered to have just the mapped
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98 reads). You could then show the different mappings (and their overlaps)
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99 as a Venn Diagram, and the outside count would be the unmapped reads.
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100
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101 **Citations**
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102
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103 The Venn Diagrams are drawn using Gordon Smyth's limma package from
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104 R/Bioconductor, http://www.bioconductor.org/
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105
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106 The R library is called from Python via rpy, http://rpy.sourceforge.net/
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107
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108 If you use this Galaxy tool in work leading to a scientific publication please
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109 cite:
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110
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111 Peter Cock, Bjoern Gruening, Konrad Paszkiewicz and Leighton Pritchard (2013).
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112 Galaxy tools and workflows for sequence analysis with applications
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113 in molecular plant pathology. PeerJ 1:e167
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114 http://dx.doi.org/10.7717/peerj.167
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115
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116 This tool uses Biopython to read and write SFF files, so you may also wish to
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117 cite the Biopython application note (and Galaxy too of course):
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118
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119 Cock et al 2009. Biopython: freely available Python tools for computational
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120 molecular biology and bioinformatics. Bioinformatics 25(11) 1422-3.
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121 http://dx.doi.org/10.1093/bioinformatics/btp163 pmid:19304878.
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122
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123 </help>
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124 </tool>