Mercurial > repos > peterjc > venn_list
annotate tools/venn_list/venn_list.xml @ 5:26e35d5133a1 draft
v0.0.9 - Tool Shed dependency for rpy and limma
author | peterjc |
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date | Sat, 10 Oct 2015 08:52:01 -0400 |
parents | 991342eca214 |
children | ea68a1a4c1d9 |
rev | line source |
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5 | 1 <tool id="venn_list" name="Venn Diagram" version="0.0.9"> |
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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> |
5 | 5 <requirement type="python-module">Bio</requirement> |
6 <requirement type="package" version="1.0.3">rpy</requirement> | |
7 <requirement type="package" version="3.25.3">limma</requirement> | |
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8 <requirement type="package" version="1.65">biopython</requirement> |
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9 </requirements> |
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10 <stdio> |
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11 <!-- Anything other than zero is an error --> |
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12 <exit_code range="1:" /> |
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13 <exit_code range=":-1" /> |
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14 </stdio> |
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15 <command interpreter="python"> |
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16 venn_list.py |
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17 #if $universe.type_select=="implicit": |
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18 - - |
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19 #else: |
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20 "$main" $main.ext |
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21 #end if |
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22 "$main_lab" |
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23 #for $s in $sets: |
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24 "$s.set" $s.set.ext "$s.lab" |
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25 #end for |
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26 $PDF |
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27 </command> |
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28 <inputs> |
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29 <param name="main_lab" size="30" type="text" value="Venn Diagram" label="Plot title"/> |
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30 <conditional name="universe"> |
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31 <param name="type_select" type="select" label="Implicit or explicit full ID list?"> |
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32 <option value="explicit">Explicit</option> |
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33 <option value="implicit">Implicit (use union of sets below)</option> |
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34 </param> |
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35 <when value="explicit"> |
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36 <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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37 </when> |
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38 <when value="implicit"/> |
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39 </conditional> |
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40 <repeat name="sets" min="1" max="3" title="Sets"> |
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41 <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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42 <param name="lab" size="30" type="text" value="Group" label="Caption for set"/> |
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43 </repeat> |
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44 </inputs> |
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45 <outputs> |
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46 <data format="pdf" name="PDF" /> |
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47 </outputs> |
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48 <tests> |
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49 <!-- Doesn't seem to work properly, manages to get two sets, both |
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50 with same FASTA file, but second with default "Group" label. --> |
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51 <test> |
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52 <param name="type_select" value="explicit"/> |
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53 <param name="main" value="venn_list.tabular" ftype="tabular"/> |
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54 <param name="main_lab" value="Some Proteins"/> |
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55 <param name="set" value="rhodopsin_proteins.fasta"/> |
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56 <param name="lab" value="Rhodopsins"/> |
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57 <output name="PDF" file="magic.pdf" ftype="pdf" compare="contains" /> |
5 | 58 <assert_stdout> |
59 <has_line line="Doing 1-way Venn Diagram" /> | |
60 <has_line line="Total of 10 IDs" /> | |
61 <has_line line="6 in Rhodopsins" /> | |
62 </assert_stdout> | |
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63 </test> |
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64 <test> |
5 | 65 <param name="type_select" value="implicit"/> |
66 <param name="sets_0|set" value="rhodopsin_proteins.fasta"/> | |
67 <param name="sets_0|lab" value="Rhodopsins"/> | |
68 <param name="sets_1|set" value="four_human_proteins.fasta"/> | |
69 <param name="sets_1|lab" value="Human"/> | |
70 <param name="sets_2|set" value="blastp_four_human_vs_rhodopsin.tabular"/> | |
71 <param name="sets_2|lab" value="Human vs Rhodopsin BLAST"/> | |
72 <output name="PDF" file="magic.pdf" ftype="pdf" compare="contains" /> | |
73 <assert_stdout> | |
74 <has_line line="Doing 3-way Venn Diagram" /> | |
75 <has_line line="Inferred total of 10 IDs" /> | |
76 <has_line line="6 in Rhodopsins" /> | |
77 <has_line line="4 in Human" /> | |
78 <has_line line="1 in Human vs Rhodopsin BLAST" /> | |
79 </assert_stdout> | |
80 </test> | |
81 <test expect_failure="true" expect_exit_code="1"> | |
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82 <param name="type_select" value="explicit"/> |
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83 <param name="main" value="venn_list.tabular" ftype="tabular"/> |
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84 <param name="main_lab" value="Some Proteins"/> |
5 | 85 <param name="sets_0|set" value="rhodopsin_proteins.fasta"/> |
86 <param name="sets_0|lab" value="Rhodopsins"/> | |
87 <param name="sets_1|set" value="four_human_proteins.fasta"/> | |
88 <param name="sets_1|lab" value="Human"/> | |
89 <param name="sets_2|set" value="blastp_four_human_vs_rhodopsin.tabular"/> | |
90 <param name="sets_2|lab" value="Human vs Rhodopsin BLAST"/> | |
91 <assert_stdout> | |
92 <has_line line="Doing 3-way Venn Diagram" /> | |
93 <has_line line="Total of 10 IDs" /> | |
94 </assert_stdout> | |
95 <assert_stderr> | |
96 <has_text_matching expression="Unexpected ID sp|Q9BS26|ERP44_HUMAN in fasta file *" /> | |
97 </assert_stderr> | |
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98 </test> |
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99 </tests> |
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100 <help> |
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101 |
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102 .. class:: infomark |
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103 |
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104 **TIP:** If your data is in tabular files, the identifier is assumed to be in column one. |
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105 |
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106 **What it does** |
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107 |
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108 Draws Venn Diagram for one, two or three sets (as a PDF file). |
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109 |
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110 You must supply one, two or three sets of identifiers -- corresponding |
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111 to one, two or three circles on the Venn Diagram. |
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112 |
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113 In general you should also give the full list of all the identifiers |
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114 explicitly. This is used to calculate the number of identifers outside |
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115 the circles (and check the identifiers in the other files match up). |
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116 The full list can be omitted by implicitly taking the union of the |
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117 category sets. In this case, the count outside the categories (circles) |
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118 will always be zero. |
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119 |
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120 The identifiers can be taken from the first column of a tabular file |
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121 (e.g. query names in BLAST tabular output, or signal peptide predictions |
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122 after filtering, etc), or from a sequence file (FASTA, FASTQ, SFF). |
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123 |
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124 For example, you may have a set of NGS reads (as a FASTA, FASTQ or SFF |
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125 file), and the results of several different read mappings (e.g. to |
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126 different references) as tabular files (filtered to have just the mapped |
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127 reads). You could then show the different mappings (and their overlaps) |
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128 as a Venn Diagram, and the outside count would be the unmapped reads. |
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129 |
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130 **Citations** |
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131 |
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132 The Venn Diagrams are drawn using Gordon Smyth's limma package from |
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133 R/Bioconductor, http://www.bioconductor.org/ |
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134 |
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135 The R library is called from Python via rpy, http://rpy.sourceforge.net/ |
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136 |
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137 If you use this Galaxy tool in work leading to a scientific publication please |
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138 cite: |
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139 |
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140 Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013). |
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141 Galaxy tools and workflows for sequence analysis with applications |
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142 in molecular plant pathology. PeerJ 1:e167 |
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143 http://dx.doi.org/10.7717/peerj.167 |
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144 |
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145 This tool uses Biopython to read and write SFF files, so you may also wish to |
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146 cite the Biopython application note (and Galaxy too of course): |
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147 |
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148 Cock et al 2009. Biopython: freely available Python tools for computational |
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149 molecular biology and bioinformatics. Bioinformatics 25(11) 1422-3. |
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150 http://dx.doi.org/10.1093/bioinformatics/btp163 pmid:19304878. |
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151 |
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152 </help> |
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153 <citations> |
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154 <citation type="doi">10.7717/peerj.167</citation> |
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155 <citation type="doi">10.1093/bioinformatics/15.5.356</citation> |
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156 </citations> |
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|
157 </tool> |