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1 <tool id="Analyze_Diff_Exp" name="Analyze_Differential_Expression" version="0.0.1">
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2
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3 <description>Analyze differential expression</description>
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4 <requirements>
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5 <requirement type="package" version="2.7">python</requirement>
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6 <requirement type="package">trinity</requirement>
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7 </requirements>
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8 <command>
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9 <![CDATA[
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10 python $__tool_directory__/analyze_diff_exp_wrapper.py $EdgeRTarGz $TMM_Matrix_FPKM $Pvalue $Cvalue
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11 ]]>
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12 </command>
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13 <inputs>
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14 <param name="EdgeRTarGz" label="EdgeR tar gz file" type="data" format="file"/>
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15 <param name="TMM_Matrix_FPKM" label="TMM Normalized FPKM matrix" type="data" format="file" />
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16 <param name="Pvalue" label="P-value" value="0.05" type="float" />
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17 <param name="Cvalue" label="C-value" value="0" type="float" />
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18
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19 </inputs>
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20 <outputs>
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21 <data format="data" name="diffExpr_matrix" label="${tool.name} on ${on_string}: Matrix" from_work_dir="diffExpr.matrix"/>
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22 <data format="data" name="diffExpr_correlation_matrix" label="${tool.name} on ${on_string}: Sample_Correlation_Matrix" from_work_dir="diffExpr.matrix.log2.sample_cor.dat"/>
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23 <data format="data" name="diffExpr_correlation_matrix_pdf" label="${tool.name} on ${on_string}: Sample_Correlation_Matrix_PDF" from_work_dir="diffExpr.matrix.log2.sample_cor_matrix.pdf"/>
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24 <data format="data" name="Heatmap" label="${tool.name} on ${on_string}: Heatmap" from_work_dir="diffExpr.matrix.log2.centered.genes_vs_samples_heatmap.pdf"/>
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25 </outputs>
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26 <tests>
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27 <test>
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28 <param name="EdgeRTarGz" value="Sp.edgeR.tar.gz" ftype="tar" />
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29 <param name="TMM_Matrix_FPKM" value="Sp.TMM.EXPR.matrix" />
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30 <param name="Pvalue" value="0.05" />
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31 <param name="Cvalue" value="0.0" />
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32
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33 <output name="diffExpr_matrix" >
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34 <assert_contents>
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35 <has_line_matching expression=".+" />
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36 <has_line line="Sp_ds	Sp_hs" />
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37 <has_line_matching expression="TRINITY_DN.+" />
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38 </assert_contents>
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39 </output>
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40 <output name="diffExpr_correlation_matrix" file="Sp.diffExpr.matrix.log2.sample_cor.dat" />
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41 <output name="diffExpr_correlation_matrix_pdf" >
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42 <assert_contents>
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43 <has_line_matching expression=".+" />
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44 </assert_contents>
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45 </output>
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46 <output name="Heatmap" >
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47 <assert_contents>
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48 <has_line_matching expression=".+" />
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49 </assert_contents>
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50 </output>
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51
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52 </test>
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53 </tests>
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54 <help>
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55 .. class:: infomark
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56
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57 This tool filters differentially expressed transcripts derived from edgeR using a minimum fold change (C-value) which will be log2 transformed before use and a required significance (P-value) in the pairwise sample comparisons (after false discovery rate correction).
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58
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59 If you are following the Trinity RNA-seq protocol please go here_ for a galaxy tool walk through or the Nature Protocols paper_.
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60
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61 .. _here: https://github.com/trinityrnaseq/GalaxyTrinityProtocol/wiki
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62 .. _paper: http://www.nature.com/nprot/journal/v8/n8/full/nprot.2013.084.html
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63 </help>
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64
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65 <citations>
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66 <citation type="doi">10.1038/nbt.1883</citation>
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67 </citations>
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68
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69 </tool>
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