Mercurial > repos > galaxyp > proteore_venn_diagram

annotate venn_diagram.xml @ 0:57f01ca855cd draft default tip

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"planemo upload commit 47d779aa1de5153673ac8bb1e37c9730210cbb5d"
author galaxyp
date Sat, 12 Jun 2021 18:06:28 +0000
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1 <?xml version="1.0"?>
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2 <tool id="proteore_venn_diagram" name="Venn diagram" version="2021.06.08" profile="20.01">
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3 <description>with JVenn</description>
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4 <requirements>
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5 <requirement type="package" version="3.9">python</requirement>
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6 </requirements>
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7 <command detect_errors="aggressive"><![CDATA[
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8 python '$__tool_directory__/venn_diagram.py'
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9
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10 #for $i, $s in enumerate($series)
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11 --input
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12 #if $s.se.input == "file"
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13 '$s.se.file' '$s.name' 'file' '$s.se.header' '$s.se.ncol'
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14 #else
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15 '$s.se.list' '$s.name' 'list'
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16 #end if
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17 #end for
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18 --summary '$output_summary'
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19 ]]></command>
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20 <inputs>
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21 <repeat name="series" title="List to compare" min="2" max="6">
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22 <conditional name="se" >
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23 <param type="select" name="input" label="Enter your list" help="Copy/paste or from a file (e.g. table)" >
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24 <option value="list">Copy/paste list </option>
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25 <option value="file" selected="true">Input file containing your list</option>
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26 </param>
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27 <when value="file">
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28 <param type="data" name="file" format="txt,tabular" label="Select your file" />
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29 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does file contain header?" />
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30 <param type="text" name="ncol" value="c1" label="Column number on which apply the comparison" help ='For example, fill in "c1" if you want to filter the first column'>
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31 <validator type="regex" message="Please enter a column number, for example: 'c1' for the first column">[c]{0,1}[0-9]+</validator>
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32 </param>
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33 </when>
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34 <when value="list">
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35 <param type="text" name="list" label="Copy/paste list" help='IDs must be separated by spaces into the form field, for example: P31946 P62258' >
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36 <sanitizer>
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37 <valid initial="string.printable">
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38 <remove value="&apos;"/>
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39 <remove value="/"/>
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40 </valid>
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41 <mapping initial="none">
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42 <add source="&apos;" target="__sq__"/>
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43 </mapping>
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44 </sanitizer>
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45 </param>
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46 </when>
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47 </conditional>
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48 <param type="text" name="name" value="" label="Enter the name of this list" help="This name will be displayed on venn diagram" optional="false">
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49 <sanitizer>
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50 <valid initial="string.printable">
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51 <remove value="&apos;"/>
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52 </valid>
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53 <mapping initial="none">
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54 <add source="&apos;" target="__sq__"/>
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55 </mapping>
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56 </sanitizer>
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57 <validator type="regex" message="Please enter a list name">[a-zA-Z0-9._-]+</validator>
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58 </param>
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59 </repeat>
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60 </inputs>
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61 <outputs>
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62 <data format="html" name="output_summary" label="Venn diagram" from_work_dir="venn_diagram_summary.html" />
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63 <data format="tsv" name="output_text" label="Venn diagram text output" from_work_dir="venn_diagram_text_output.tsv" />
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64 </outputs>
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65 <tests>
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66 <test>
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67 <repeat name="series">
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68 <conditional name="se">
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69 <param name="input" value="file" />
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70 <param name="file" value="ID_Converter_FKW_Lacombe_et_al_2017_OK.txt" />
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71 <param name="header" value="true" />
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72 <param name="ncol" value="c1" />
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73 </conditional>
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74 <param name="name" value="Lacombe" />
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75 </repeat>
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76 <repeat name="series">
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77 <conditional name="se">
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78 <param name="input" value="file" />
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79 <param name="file" value="Bredberg.txt" />
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80 <param name="header" value="false" />
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81 <param name="ncol" value="c1" />
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82 </conditional>
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83 <param name="name" value="Bredberg" />
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84 </repeat>
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85 <repeat name="series">
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86 <conditional name="se">
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87 <param name="input" value="file" />
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88 <param name="file" value="Mucilli.txt" />
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89 <param name="header" value="false" />
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90 <param name="ncol" value="c1" />
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91 </conditional>
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92 <param name="name" value="Mucilli" />
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93 </repeat>
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94 <output name="output_summary" file="Venn_diagram_html.html" />
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95 <!-- <output name="output_text" file="Venn_text_output.txt" /> -->
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96 </test>
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97 </tests>
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98 <help><![CDATA[
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99
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100 **Description**
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101
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102 This tool is used for cross-comparison purpose between several lists having a common key (e.g. IDs) and draw a venn diagram from lists/files using the Jvenn plug-in (see Authors below).
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103 It also creates output text file that contain common or specific elements between query and each compared lists/files.
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104
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105 -----
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106
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107 **Input**
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108
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109 Can be either a list entered in a copy/paste mode or a single or multi-columns file (txt, tsv, csv, tab, output from other tools) up to six lists/files
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110
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111 * **List of IDs in a copy/paste mode:** IDs have to be separated by a space (e.g. AMY1A ALB IGKC CSTA IGHA1 ACTG1)
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112
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113 * **for example an IDs list file** in .txt format, with 1 ID per line
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114
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115 .. csv-table:: tab1
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116 :header: "Ids"
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117
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118
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119 "AMY1A"
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120 "ALB"
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121 "IGKC"
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122 "CSTA"
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123 "IGHA1"
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124
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125 If you use a file as input list, it is necessary to specify the column number on which to apply the comparison.
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126
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127 Ids in a line will be split by ";", so if you have this kind of input :
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128
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129 .. csv-table:: tab with multiple ids per line
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130 :header: "Ids"
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131
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132 "P22531"
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133 "P04792"
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134 "P01834"
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135 "Q96KK5"
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136 "Q06830;P60709;P13646;P31949"
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137 "P06702"
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138 "P14923"
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139 "Q13835"
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140
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141 All ID will be considered (i.e. Q06830,P60709,P13646 and P31949 will be split).
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142
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143 .. class:: warningmark
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144
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145 In copy/paste mode, the number of IDs considered in input is limited to 5000.
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146
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147 -----
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148
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149 **Parameter**
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150
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151 "Please enter the name of this list": each list or set should be named, this information will be reported in both output (see below)
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152
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153 -----
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154
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155 **Output**
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156
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157 Two outputs are generated:
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158
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159 * **Graphical file**: Venn diagram that you can either display (interactive mode) or download as an image (PNG, SVG format)
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160
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161 * **Venn text output file** : a text file containing specific elements or shared by lists/files.
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162
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163
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164 ]]></help>
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165 <citations>
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166 <citation type="doi">doi:10.1186/1471-2105-15-293</citation>
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167 <citation type="bibtex">@book{toolsProteoRE,
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168 journal = {GitHub repository},
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169 publisher = {GitHub},
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170 title = {ProteoRE tools},
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171 url = {https://github.com/galaxyproteomics/tools-galaxyp},
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172 author = {Lien Nguyen, David Chistiany, Florence Combes,Christophe Caron, Valentin Loux Yves Vandenbrouck},
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173 date = {2021},
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174 year = {2021},
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175 }</citation>
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176 </citations>
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177 </tool>