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1 <tool id="Get_Datasets" name="Query GEO Database" version="20181028">
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2 <description> Query Gene Expression Omnibus (GEO) Database using accession code. </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="2.42.0">bioconductor-geoquery</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__/GetDatasets.R' GeoCode $GeoCode
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11 ]]>
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12 </command>
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13 <inputs>
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14 <param name="GeoCode" size="40" type="text" value="GSE50628" label="GEO accession" help="Gene Expression Omnibus (GEO) accession code">
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15 <sanitizer>
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16 <valid initial="string.printable,string.digits">
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17 </valid>
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18 </sanitizer>
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19 </param>
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20 </inputs>
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21 <outputs>
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22 <data format="microarray" type="microarray" name="Geo Raw">
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23 <discover_datasets pattern="(?P<name>.*)" ext="microarray" format="microarray" type="microarray" visible="true" assign_primary_output="true" directory="CEL" />
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24 </data>
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25 </outputs>
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26 <stdio>
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27 <exit_code range="1:" level="fatal" />
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28 </stdio>
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29 <help>
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30
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31 .. class:: infomark
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32
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33 **Authors** Bensellak Taoufik bensellak.taoufik@gmail.com, El Messaoudi Idrissi Mohcine mohcine.elmessaoudi@gmail.com , Ahmed Moussa ahmed.moussa2@gmail.com .
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34
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35 ---------------------------------------------------
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36
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37 ==================================================================
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38 Query Gene Expression Omnibus (GEO) Database.
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39 ==================================================================
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40
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41 -----------
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42 Description
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43 -----------
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44
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45 This tool is used for querying Gene Expression Omnibus Database.
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46
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47 **GEO accession**
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48
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49 GEO Accession code
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50
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51 -----------------
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52 Workflow position
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53 -----------------
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54
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55 **Upstream tools**
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56
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57 +------------------------+------------------+--------+-----------+
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58 | Name | output file |format | parameter |
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59 +========================+==================+========+===========+
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60 | NA | NA | NA | NA |
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61 +------------------------+------------------+--------+-----------+
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62
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63
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64 **Downstream tools**
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65
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66 +-----------------------------------------------+------------------------------------------------+------------+
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67 | Name | Output file | Format |
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68 +===============================================+================================================+============+
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69 | Create Desig | DataSet.Design.tsv,DataSet.Informations.RData | tsv,RData |
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70 +-----------------------------------------------+------------------------------------------------+------------+
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71
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72 -----------
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73 Input files
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74 -----------
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75
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76 +---------------------------+------------+
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77 | Parameter : num + label | Format |
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78 +===========================+============+
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79 | GEO accession | String |
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80 +---------------------------+------------+
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81
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82 ------------
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83 Output files
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84 ------------
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85
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86 **Set of raw samples**
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87
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88 ------------------------------
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89 General schema of the workflow
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90 ------------------------------
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91
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92 .. image:: ./workflow.jpg
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93 :height: 800
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94 :width: 700
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95
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96 </help>
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97 </tool>
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