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1 <tool id="Format_Dream" name="Dream Tabular" version="20181019" hidden="false">
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2 <description> Read DataSet into Rdata Binary for the Preprocessing Step. </description>
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3 <requirements>
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4 <requirement type="package" version="3.4.1_0">r-base</requirement>
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5 <requirement type="package" version="1.1_4">r-batch</requirement>
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6 <requirement type="package" version="1.11.4" owner="defaults">r-data.table</requirement>
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7 </requirements>
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8 <command>
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9 <![CDATA[
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10 Rscript '$__tool_directory__/FormatDream.R'
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11 datasetsource $inputdata
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12 ]]>
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13
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14 </command>
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15 <inputs>
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16 <param name="inputdata" type="data" format="tabular" label="Select File."/>
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17
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18 </inputs>
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19 <outputs>
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20 <data name="Format_Dream.tsv" format="tabular" from_work_dir="Format_Dream.tsv" label="Format_Dream.tsv">
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21 </data>
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22 </outputs>
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23 <stdio>
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24 <exit_code range="1:" level="fatal" />
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25 </stdio>
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26 <help>
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27
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28 .. class:: infomark
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29
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30 **Authors** Bensellak Taoufik bensellak@ensat.ac.ma, El Messaoudi Idrissi Mohcine mohcine.elmessaoudi@gmail.com, Ahmed Moussa ahmed.moussa2@gmail.com .
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31
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32 ---------------------------------------------------
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33
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34 ==================================
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35 Read Microarray DataSet
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36 ==================================
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37
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38 -----------
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39 Description
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40 -----------
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41
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42 This tool is used for reading choosen dataset in order to process, dataset could be imported or selected from available datasets.
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43
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44 -----------------
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45 Workflow position
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46 -----------------
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47
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48 **Upstream tools**
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49
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50 +------------------------+--------------------------------------------------+--------+
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51 | Name | output file |format |
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52 +========================+==================================================+========+
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53 | Get List Datasets | Projects.Informations.on.technology.RData | Rdata |
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54 +------------------------+--------------------------------------------------+--------+
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55 | Get List Datasets | Get.List.DataSets.Microarrays.on.technology.tsv | Tabular|
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56 +------------------------+--------------------------------------------------+--------+
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57 | Make Design | Imported.Project.Informations.RData | Rdata |
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58 +------------------------+--------------------------------------------------+--------+
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59
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60
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61 **Downstream tools**
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62
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63 +-------------------------------------------+----------------------------------+----------+
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64 | Name | Output file | Format |
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65 +===========================================+==================================+==========+
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66 |Preprocess.DataSet.Microarray | Preprocess.Project.Data.RData | RData |
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67 +-------------------------------------------+----------------------------------+----------+
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68 |Matrix.Data | Matrix.Data.tsv | Tabular |
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69 +-------------------------------------------+----------------------------------+----------+
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70
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71 -----------
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72 Input files
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73 -----------
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74
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75 +---------------------------------+------------+
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76 | Parameter : num + label | Format |
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77 +=================================+============+
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78 | image (both intern and exterm ) | Rdata |
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79 +---------------------------------+------------+
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80 | datasetsnames (only intern) | Tabular |
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81 +---------------------------------+------------+
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82
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83 ------------
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84 Output files
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85 ------------
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86
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87 **MicroArrayObject.RData** Both for intern and extern datasets
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88
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89 **design.tsv** Only for extern datasets
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90
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91 ------------------------------
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92 General schema of the workflow
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93 ------------------------------
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94
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95 .. image:: ./images/workflow.jpg
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96 :height: 800
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97 :width: 700
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98
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99 </help>
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100 </tool>
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