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1 <tool id="GEOQuery" name="GEOQuery">
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2 <description>GEOQuery wrapper</description>
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3 <requirements>
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4 <container type="docker">sblanck/smat</container>
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5 </requirements>
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6 <command>
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7 /galaxy-tools/stderr_wrapper.py Rscript
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8 /galaxy-tools/transcriptomics/GEOquery/GEOQuery.R
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9 $GEOQueryID
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10 $GEOQueryData
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11 $GEOQueryRData
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12 $conditions
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13 $transformation
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14 </command>
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15
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16 <inputs>
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17 <param name="GEOQueryID" type="text" size="12" optional="false" label="GEOQuery ID" help="">
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18 <validator type="empty_field"/>
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19 </param>
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20 <param name="transformation" type="select" label="log2 transformation">
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21 <option value="auto">auto</option>
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22 <option value="yes">yes</option>
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23 <option value="no">no</option>
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24 </param>
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25 </inputs>
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26
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27 <outputs>
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28 <data format="tabular" name="GEOQueryData" label="GEOQuery Data of ${GEOQueryID}"/>
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29 <data format="cond" name="conditions" label="conditions of ${GEOQueryID}"/>
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30 <data format="rdata" name="GEOQueryRData" label="GEOQuery RData of ${GEOQueryID}"/>
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31 </outputs>
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32 <help>
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33 **What it does**
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34
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35 This tool fetches microarray data directly from GEO database, based on the GEOQuery R package. Given a GSE accession ID, it returns an Rdata object containing the data and a text file (.cond file) summarizing the conditions of the experiment.
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36 The .cond file is a text file containing one line per sample in the experiment. Each line is made of 3 columns:
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37
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38 - Sample ID
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39 - Condition of the biological sample
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40 - Description of the biological sample
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41
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42 **Example** of .cond file
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43 ::
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44
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45 Sample ID Condition Description
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46 GSM80460 series of 16 tumors GSM80460 OSCE-2T SERIES OF 16 TUMORS
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47 GSM80461 series of 16 tumors GSM80461 OSCE-4T Series of 16 Tumors
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48 GSM80462 series of 16 tumors GSM80462 OSCE-6T Series of 16 Tumors
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49 GSM80476 series of 4 normals GSM80476 OSCE-2N Series of 4 Normals
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50 GSM80477 series of 4 normals GSM80477 OSCE-9N Series of 4 Normals
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51
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52 **Results**
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53
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54 - Rdata object containing data for further analysis
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55 - Condition (.cond) file summarizing conditions of the experiment
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56 - Tabular (.txt) file containing expression data for each sample
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57
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58
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59 </help>
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60
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61
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62 </tool>
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