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planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 7026b0fbe3611962c37c7f9b5f001434f059e32c
author sblanck
date Tue, 26 Jun 2018 04:14:25 -0400
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1 <tool id="GEOQuery" name="GEOQuery" version="1.0.0">
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3 <description>GEOQuery wrapper</description>
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5 <requirements>
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6 <requirement type="package" version="2.46.0">bioconductor-geoquery</requirement>
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7 <requirement type="package">r-optparse</requirement>
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8 </requirements>
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9 <stdio>
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10 <exit_code range="1:" />
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11 <regex match="Warning" source="both" level="warning"/>
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12 </stdio>
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13
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14 <command>
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15 <![CDATA[
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16 Rscript --vanilla
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17 ${__tool_directory__}/GEOQuery.R
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18 --id ${GEOQueryID}
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19 --transformation ${transformation}
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20 --data ${GEOQueryData}
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21 --rdata ${GEOQueryRData}
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22 --conditions ${conditions}
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23 ]]>
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24 </command>
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25
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26 <inputs>
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27 <param name="GEOQueryID" type="text" size="12" optional="false" label="GEOQuery ID" help="">
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28 <validator type="empty_field"/>
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29 </param>
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30 <param name="transformation" type="select" label="log2 transformation">
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31 <option value="auto">auto</option>
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32 <option value="yes">yes</option>
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33 <option value="no">no</option>
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34 </param>
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35 </inputs>
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36
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37 <outputs>
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38 <data format="tabular" name="GEOQueryData" label="GEOQuery Data of ${GEOQueryID}"/>
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39 <data format="cond" name="conditions" label="conditions of ${GEOQueryID}"/>
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40 <data format="rdata" name="GEOQueryRData" label="GEOQuery RData of ${GEOQueryID}"/>
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41 </outputs>
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43 <tests>
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44 <test>
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45 <param name="GEOQueryID" value="GSE3524"/>
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46 <param name="transformation" value="auto"/>
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47 <output name="conditions" file="conditions.cond" ftype="cond"/>
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48 </test>
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49 </tests>
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50
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51 <help>
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52 <![CDATA[
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53 **What it does**
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55 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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56 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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57
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58 - Sample ID
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59 - Condition of the biological sample
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60 - Description of the biological sample
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61
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62 **Example** of .cond file
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63 ::
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65 GSM80460 series of 16 tumors GSM80460 OSCE-2T SERIES OF 16 TUMORS
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66 GSM80461 series of 16 tumors GSM80461 OSCE-4T Series of 16 Tumors
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67 GSM80462 series of 16 tumors GSM80462 OSCE-6T Series of 16 Tumors
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68 GSM80476 series of 4 normals GSM80476 OSCE-2N Series of 4 Normals
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69 GSM80477 series of 4 normals GSM80477 OSCE-9N Series of 4 Normals
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71 **Results**
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73 - Rdata object containing data for further analysis
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74 - Condition (.cond) file summarizing conditions of the experiment
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75 - Tabular (.txt) file containing expression data for each sample
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76 ]]>
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77 </help>
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79 </tool>