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1 <?xml version="1.0" encoding="UTF-8"?>
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2 <tool id="edger_dge" name="edgeR Differential GeneExpression Analysis">
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3 <description>RNA-Seq expression analysis using edgeR (R package)</description>
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4
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5 <command>
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6 <!--
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7 The following script is written in the "Cheetah" language:
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8 http://www.cheetahtemplate.org/docs/users_guide_html_multipage/contents.html
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9 -->
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10
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11 R CMD BATCH --vanilla '--args
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12 $design_matrix
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13 $contrast
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14
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15 $output_count_edgeR
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16 $output_cpm
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17 output_FPXM
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18 $output_raw_counts
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19
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20 $qc
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21 $output_MDSplot
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22 $output_BCVplot
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23 $output_MAplot
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24 smearPlot '
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25 /home/youri/Desktop/galaxy/tools/TraIT/edgeR/DGE/edgeR_DGE_test.R $output_R
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26 </command>
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27
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28 <inputs>
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29 <param name="design_matrix" type="data" format="tabular" help="Design matrix" />
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30
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31 <param name="contrast" type="text" label="Contrast (biological question)" help="e.g. 'tumor-normal' or '(G1+G2)/2-G3' using the factors chosen in the design matrix. Read the 'makeContrasts' manual from Limma package for more info." />
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32
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33 <param name="qc" type="select" label="Quality control reports">
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34 <option value="true">Yes</option>
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35 <option value="false" selected="true">No</option>
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36 </param>
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37
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38 <param name="debug" type="select" label="R Debug output">
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39 <option value="true" selected="true"> Yes</option>
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40 <option value="false">No</option>
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41 </param>
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42 </inputs>
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43
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44 <outputs>
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45 <data format="tabular" name="output_count_edgeR" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - table" />
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46 <data format="tabular" name="output_cpm" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - CPM" />
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47 <data format="tabular" name="output_raw_counts" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - raw counts" />
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48
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49 <data format="txt" name="output_R" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - R output" >
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50 <filter>(debug == "true")</filter>
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51 </data>
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52
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53 <data format="pdf" name="output_MDSplot" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - MDS-plot">
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54 <filter>(qc == "true")</filter>
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55 </data>
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56
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57 <data format="pdf" name="output_BCVplot" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - BCV-plot">
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58 <filter>(qc == "true")</filter>
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59 </data>
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60
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61 <data format="pdf" name="output_MAplot" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - MA-plot">
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62 <filter>(qc == "true")</filter>
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63 </data>
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64 </outputs>
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65
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66 <help>
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67 input: Design matrix using "create Design matrix" tool
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68 input: contrast
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69 </help>
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70 </tool>
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