Mercurial > repos > peterjc > venn_list
annotate tools/venn_list/venn_list.xml @ 6:ea68a1a4c1d9 draft
v0.0.10 explicit galaxy_sequence_utils dependency etc
author | peterjc |
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date | Thu, 02 Feb 2017 11:17:31 -0500 |
parents | 26e35d5133a1 |
children | ba31415fedc5 |
rev | line source |
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1 <tool id="venn_list" name="Venn Diagram" version="0.0.10"> |
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2 <description>from lists</description> |
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3 <requirements> |
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4 <requirement type="package" version="1.0.1">galaxy_sequence_utils</requirement> |
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5 <requirement type="python-module">rpy</requirement> |
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6 <requirement type="python-module">Bio</requirement> |
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7 <requirement type="package" version="1.0.3">rpy</requirement> |
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8 <requirement type="package" version="3.25.3">limma</requirement> |
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9 <requirement type="package" version="1.65">biopython</requirement> |
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10 </requirements> |
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11 <stdio> |
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12 <!-- Anything other than zero is an error --> |
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13 <exit_code range="1:" /> |
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14 <exit_code range=":-1" /> |
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15 </stdio> |
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16 <command interpreter="python"> |
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17 venn_list.py |
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18 #if $universe.type_select=="implicit": |
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19 - - |
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20 #else: |
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21 "$main" $main.ext |
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22 #end if |
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23 "$main_lab" |
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24 #for $s in $sets: |
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25 "$s.set" $s.set.ext "$s.lab" |
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26 #end for |
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27 $PDF |
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28 </command> |
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29 <inputs> |
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30 <param name="main_lab" size="30" type="text" value="Venn Diagram" label="Plot title"/> |
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31 <conditional name="universe"> |
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32 <param name="type_select" type="select" label="Implicit or explicit full ID list?"> |
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33 <option value="explicit">Explicit</option> |
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34 <option value="implicit">Implicit (use union of sets below)</option> |
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35 </param> |
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36 <when value="explicit"> |
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37 <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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38 </when> |
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39 <when value="implicit"/> |
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40 </conditional> |
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41 <repeat name="sets" min="1" max="3" title="Sets"> |
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42 <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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43 <param name="lab" size="30" type="text" value="Group" label="Caption for set"/> |
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44 </repeat> |
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45 </inputs> |
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46 <outputs> |
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47 <data format="pdf" name="PDF" /> |
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48 </outputs> |
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49 <tests> |
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50 <!-- Doesn't seem to work properly, manages to get two sets, both |
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51 with same FASTA file, but second with default "Group" label. --> |
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52 <test> |
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53 <param name="type_select" value="explicit"/> |
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54 <param name="main" value="venn_list.tabular" ftype="tabular"/> |
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55 <param name="main_lab" value="Some Proteins"/> |
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56 <param name="set" value="rhodopsin_proteins.fasta"/> |
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57 <param name="lab" value="Rhodopsins"/> |
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58 <output name="PDF" file="magic.pdf" ftype="pdf" compare="contains" /> |
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59 <assert_stdout> |
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60 <has_line line="Doing 1-way Venn Diagram" /> |
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61 <has_line line="Total of 10 IDs" /> |
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62 <has_line line="6 in Rhodopsins" /> |
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63 </assert_stdout> |
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64 </test> |
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65 <test> |
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66 <param name="type_select" value="implicit"/> |
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67 <param name="sets_0|set" value="rhodopsin_proteins.fasta"/> |
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68 <param name="sets_0|lab" value="Rhodopsins"/> |
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69 <param name="sets_1|set" value="four_human_proteins.fasta"/> |
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70 <param name="sets_1|lab" value="Human"/> |
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71 <param name="sets_2|set" value="blastp_four_human_vs_rhodopsin.tabular"/> |
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72 <param name="sets_2|lab" value="Human vs Rhodopsin BLAST"/> |
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73 <output name="PDF" file="magic.pdf" ftype="pdf" compare="contains" /> |
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74 <assert_stdout> |
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75 <has_line line="Doing 3-way Venn Diagram" /> |
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76 <has_line line="Inferred total of 10 IDs" /> |
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77 <has_line line="6 in Rhodopsins" /> |
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78 <has_line line="4 in Human" /> |
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79 <has_line line="1 in Human vs Rhodopsin BLAST" /> |
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80 </assert_stdout> |
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81 </test> |
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82 <test expect_failure="true" expect_exit_code="1"> |
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83 <param name="type_select" value="explicit"/> |
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84 <param name="main" value="venn_list.tabular" ftype="tabular"/> |
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85 <param name="main_lab" value="Some Proteins"/> |
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86 <param name="sets_0|set" value="rhodopsin_proteins.fasta"/> |
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87 <param name="sets_0|lab" value="Rhodopsins"/> |
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88 <param name="sets_1|set" value="four_human_proteins.fasta"/> |
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89 <param name="sets_1|lab" value="Human"/> |
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90 <param name="sets_2|set" value="blastp_four_human_vs_rhodopsin.tabular"/> |
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91 <param name="sets_2|lab" value="Human vs Rhodopsin BLAST"/> |
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92 <assert_stdout> |
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93 <has_line line="Doing 3-way Venn Diagram" /> |
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94 <has_line line="Total of 10 IDs" /> |
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95 </assert_stdout> |
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96 <assert_stderr> |
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97 <has_text_matching expression="Unexpected ID sp|Q9BS26|ERP44_HUMAN in fasta file *" /> |
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98 </assert_stderr> |
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99 </test> |
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100 </tests> |
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101 <help> |
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102 |
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103 .. class:: infomark |
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104 |
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105 **TIP:** If your data is in tabular files, the identifier is assumed to be in column one. |
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106 |
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107 **What it does** |
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108 |
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109 Draws Venn Diagram for one, two or three sets (as a PDF file). |
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110 |
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111 You must supply one, two or three sets of identifiers -- corresponding |
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112 to one, two or three circles on the Venn Diagram. |
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113 |
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114 In general you should also give the full list of all the identifiers |
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115 explicitly. This is used to calculate the number of identifers outside |
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116 the circles (and check the identifiers in the other files match up). |
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117 The full list can be omitted by implicitly taking the union of the |
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118 category sets. In this case, the count outside the categories (circles) |
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119 will always be zero. |
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120 |
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121 The identifiers can be taken from the first column of a tabular file |
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122 (e.g. query names in BLAST tabular output, or signal peptide predictions |
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123 after filtering, etc), or from a sequence file (FASTA, FASTQ, SFF). |
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124 |
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125 For example, you may have a set of NGS reads (as a FASTA, FASTQ or SFF |
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126 file), and the results of several different read mappings (e.g. to |
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127 different references) as tabular files (filtered to have just the mapped |
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128 reads). You could then show the different mappings (and their overlaps) |
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129 as a Venn Diagram, and the outside count would be the unmapped reads. |
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130 |
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131 **Citations** |
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132 |
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133 The Venn Diagrams are drawn using Gordon Smyth's limma package from |
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134 R/Bioconductor, http://www.bioconductor.org/ |
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135 |
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136 The R library is called from Python via rpy, http://rpy.sourceforge.net/ |
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137 |
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138 If you use this Galaxy tool in work leading to a scientific publication please |
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139 cite: |
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140 |
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141 Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013). |
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142 Galaxy tools and workflows for sequence analysis with applications |
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143 in molecular plant pathology. PeerJ 1:e167 |
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144 http://dx.doi.org/10.7717/peerj.167 |
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145 |
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146 This tool uses Biopython to read and write SFF files, so you may also wish to |
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147 cite the Biopython application note (and Galaxy too of course): |
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148 |
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149 Cock et al 2009. Biopython: freely available Python tools for computational |
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150 molecular biology and bioinformatics. Bioinformatics 25(11) 1422-3. |
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151 http://dx.doi.org/10.1093/bioinformatics/btp163 pmid:19304878. |
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152 |
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153 </help> |
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154 <citations> |
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155 <citation type="doi">10.7717/peerj.167</citation> |
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156 <citation type="doi">10.1093/bioinformatics/15.5.356</citation> |
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157 </citations> |
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158 </tool> |