Mercurial > repos > proteore > proteore_venn_diagram

annotate venn_diagram.xml @ 0:9d4f20618ab4 draft

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author proteore
date Sun, 26 Nov 2017 19:09:40 -0500
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children 760470ddb9ca
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1 <?xml version="1.0"?>
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2 <tool id="Jvenn" name="Venn diagram" version="1.0">
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3 <description>compare lists plotting Venn Diagram (based on Jvenn).
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4 </description>
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5 <command><![CDATA[
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6 python $__tool_directory__/venn_diagram.py
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7
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8 #for $i, $s in enumerate($series)
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9 --input
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10 #if $s.se.input == "file"
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11 "$s.se.file" "$s.se.name" "file" "$s.se.header" "$s.se.ncol"
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12 #else
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13 "$s.se.list" "$s.se.name" "list"
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14 #end if
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15 #end for
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16 --summary "$output_summary"
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17 ]]></command>
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18 <inputs>
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19 <!-- Files -->
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20 <repeat name="series" title="Lists to compare" min="2" max="6" >
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21 <conditional name="se" >
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22 <param type="select" name="input" label="Please provide your identifiers" help="Copy/paste or ID list from a file (e.g. table)" >
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23 <option value="list">Copy/paste your identifiers </option>
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24 <option value="file">Input file containing your identifiers</option>
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25
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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="Choose a file that contains your list of IDs" />
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29 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does your input file contain header?" />
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30 <param type="text" name="ncol" value="c1" label="Please specify the column where you would like to apply the comparison" help ='For example, fill in "c1" if you want to filter the first column' />
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31 <param type="text" name="name" value="" label="Please enter the name of this list" help="This name will be displayed on venn diagram" />
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32 </when>
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33 <when value="list">
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34 <param type="text" name="list" label="Copy/paste your identifiers" help='IDs must be separated by spaces into the form field, for example: P31946 P62258' >
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35 <sanitizer>
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36 <valid initial="string.printable">
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37 <remove value="&apos;"/>
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38 </valid>
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39 <mapping initial="none">
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40 <add source="&apos;" target="__sq__"/>
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41 </mapping>
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42 </sanitizer>
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43 </param>
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44 <param type="text" name="name" value="" label="Please enter the name of this list" help="This name will be displayed on venn diagram" />
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45 </when>
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46 </conditional>
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47 </repeat>
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48 </inputs>
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49 <outputs>
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50 <data format="html" name="output_summary" label="Venn diagram" from_work_dir="venn_diagram_summary.html" />
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51 <data format="tabular" name="output_text" label="Venn diagram text output" from_work_dir="venn_diagram_text_output.txt" />
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52 </outputs>
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53 <tests>
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54 <test>
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55 <repeat name="series">
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56 <conditional name="se">
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57 <param name="input" value="mq_file" />
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58 <param name="mq_file" value="DESeq.txt" />
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59 <param name="header" value="false" />
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60 <param name="ncol" value="c1" />
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61 <param name="name" value="DESeq" />
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62 </conditional>
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63 </repeat>
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64 <repeat name="series">
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65 <conditional name="se">
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66 <param name="input" value="mq_file" />
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67 <param name="mq_file" value="FQ.txt" />
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68 <param name="header" value="false" />
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69 <param name="ncol" value="c1" />
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70 <param name="name" value="FQ" />
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71 </conditional>
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72 </repeat>
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73 <repeat name="series">
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74 <conditional name="se">
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75 <param name="input" value="mq_file" />
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76 <param name="mq_file" value="RPKM.txt" />
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77 <param name="header" value="false" />
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78 <param name="ncol" value="c1" />
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79 <param name="name" value="RPKM" />
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80 </conditional>
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81 </repeat>
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82 <repeat name="series">
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83 <conditional name="se">
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84 <param name="input" value="mq_file" />
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85 <param name="mq_file" value="TC.txt" />
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86 <param name="header" value="false" />
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87 <param name="ncol" value="c1" />
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88 <param name="name" value="TC" />
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89 </conditional>
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90 </repeat>
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91 <repeat name="series">
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92 <conditional name="se">
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93 <param name="input" value="mq_file" />
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94 <param name="mq_file" value="TMM.txt" />
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95 <param name="header" value="false" />
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96 <param name="ncol" value="c1" />
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97 <param name="name" value="TMM" />
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98 </conditional>
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99 </repeat>
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100 <repeat name="series">
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101 <conditional name="se">
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102 <param name="input" value="mq_file" />
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103 <param name="mq_file" value="UQ.txt" />
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104 <param name="header" value="false" />
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105 <param name="ncol" value="c1" />
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106 <param name="name" value="UQ" />
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107 </conditional>
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108 </repeat>
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109 <output name="output_summary" file="venn_diagram_summary.html" />
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110 <output name="output_text" file="venn_diagram_text_output.txt" />
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111
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112 </test>
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113 </tests>
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114 <help>
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115
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116 This tool draw a venn diagram from lists/files using Jvenn plug-in (http://jvenn.toulouse.inra.fr/app/index.html). It also creates output files that contain common or specific elements between query and each compared lists/files.
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117
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118 **Inputs**
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119
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120 * **Query file:** A file containing different information of proteins, could be output of previous components.
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121
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122 * **File of a list of IDs:** .TXT format, each line contains 1 ID
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123
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124 AMY1A
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125
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126 ALB
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127
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128 IGKC
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129
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130 CSTA
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131
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132 IGHA1
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133
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134 ACTG1
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135
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136 * **List of IDs:** IDs separated by a space
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137 AMY1A ALB IGKC CSTA IGHA1 ACTG1
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138
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139 If you choose a file, it is necessary to specify the column where you would like to perform the comparison.
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140
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141 **Outputs**
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142
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143 * **Summary file** (venn_diagram_summary.html):
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144 Venn diagram: Could be downloaded as image (PNG, SVG)
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145
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146 * **Venn text output file**
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147 A text file containing common/specific elements among compared lists/files.
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148
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149 -----
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150
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151 .. class:: infomark
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152
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153 **Authors**
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154
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155 Philippe Bardou, Jérôme Mariette, Frédéric Escudié, Christophe Djemiel and Christophe Klopp. jvenn: an interactive Venn diagram viewer. BMC Bioinformatics 2014, 15:293 doi:10.1186/1471-2105-15-293
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156
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157 .. class:: infomark
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158
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159 **Galaxy integration**
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160
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161 T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR
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162
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163 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit,Migale Bioinformatics platform
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164
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165 Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool.
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166
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167 </help>
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168 <citations>
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169 </citations>
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170 </tool>