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annotate ctat_analyze_differential_expression.xml @ 3:68c6c52d2ced draft

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author trinity_ctat
date Thu, 28 Jun 2018 22:45:26 -0400
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1 <tool id="ctat_analyze_differential_expression" name="ctat_analyze_differential_expression" version="1.0.0" profile="17.05">
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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">subprocess32</requirement>
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7 <requirement type="package">bzip2</requirement>
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8 <requirement type="package" version="1.3.0">rsem</requirement>
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9 <requirement type="package" version="3">bioconductor-edger</requirement>
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10 <requirement type="package" version="2">bioconductor-qvalue</requirement>
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11 <requirement type="package">r-cluster</requirement>
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12 <requirement type="package">r-fastcluster</requirement>
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13 <requirement type="package" version="2.6.6">trinity</requirement>
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14 </requirements>
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15 <command detect_errors="exit_code">
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16 <![CDATA[
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17 python $__tool_directory__/ctat_analyze_differential_expression.py $Counts_matrix $TMM_Matrix_FPKM $Pvalue $Cvalue
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18 ]]>
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19 </command>
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20 <inputs>
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21 <param name="EdgeRTarGz" label="EdgeR tar gz file" type="data" format="txt"/>
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22 <param name="Counts_matrix" label="Counts Matrix" type="data" format="tabular" />
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23 <param name="Pvalue" label="P-value" value="0.05" type="float" />
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24 <param name="Cvalue" label="C-value" value="0" type="float" />
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25
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26 </inputs>
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27 <outputs>
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28 <data format="data" name="diffExpr_matrix" label="${tool.name} on ${on_string}: Matrix" from_work_dir="diffExpr.matrix"/>
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29 <data format="data" name="diffExpr_correlation_matrix" label="${tool.name} on ${on_string}: Sample_Correlation_Matrix" from_work_dir="diffExpr.matrix.log2.sample_cor.dat"/>
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30 <data format="data" name="diffExpr_correlation_matrix_pdf" label="${tool.name} on ${on_string}: Sample_Correlation_Matrix_PDF" from_work_dir="diffExpr.matrix.log2.sample_cor_matrix.pdf"/>
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31 <data format="data" name="Heatmap" label="${tool.name} on ${on_string}: Heatmap" from_work_dir="diffExpr.matrix.log2.centered.genes_vs_samples_heatmap.pdf"/>
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32 </outputs>
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33 <tests>
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34 <test>
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35 <param name="EdgeRTarGz" value="Sp.edgeR.tar.gz" ftype="tar" />
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36 <param name="TMM_Matrix_FPKM" value="Sp.TMM.EXPR.matrix" />
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37 <param name="Pvalue" value="0.05" />
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38 <param name="Cvalue" value="0.0" />
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39
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40 <output name="diffExpr_matrix" >
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41 <assert_contents>
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42 <has_line_matching expression=".+" />
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43 <has_line line="Sp_ds&#009;Sp_hs" />
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44 <has_line_matching expression="TRINITY_DN.+" />
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45 </assert_contents>
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46 </output>
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47 <output name="diffExpr_correlation_matrix" file="Sp.diffExpr.matrix.log2.sample_cor.dat" />
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48 <output name="diffExpr_correlation_matrix_pdf" >
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49 <assert_contents>
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50 <has_line_matching expression=".+" />
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51 </assert_contents>
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52 </output>
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53 <output name="Heatmap" >
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54 <assert_contents>
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55 <has_line_matching expression=".+" />
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56 </assert_contents>
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57 </output>
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58
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59 </test>
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60 </tests>
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61 <help>
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62 .. class:: infomark
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63
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64 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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65
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66 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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67
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68 .. _here: https://github.com/trinityrnaseq/GalaxyTrinityProtocol/wiki
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69 .. _paper: http://www.nature.com/nprot/journal/v8/n8/full/nprot.2013.084.html
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70 </help>
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71
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72 <citations>
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73 <citation type="doi">10.1038/nbt.1883</citation>
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74 </citations>
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75
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76 </tool>