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annotate ctat_analyze_differential_expression.xml @ 0:6a8dadcd45e3 draft

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Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool.
author trinity_ctat
date Thu, 12 Apr 2018 10:10:11 -0400
parents
children 03155bc11cff
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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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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">subprocess32</requirement>
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7 <requirement type="package">samtools</requirement>
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8 <requirement type="package">bzip2</requirement>
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9 <requirement type="package" version="1.3.0">rsem</requirement>
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10 <requirement type="package" version="3">bioconductor-edger</requirement>
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11 <requirement type="package" version="2">bioconductor-qvalue</requirement>
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12 <requirement type="package" version="2.5.1">trinity</requirement>
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13 </requirements>
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14 <command detect_errors="exit_code">
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15 <![CDATA[
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16 python $__tool_directory__/ctat_analyze_diff_exp_wrapper.py $EdgeRTarGz $TMM_Matrix_FPKM $Pvalue $Cvalue
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17 ]]>
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18 </command>
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19 <inputs>
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20 <param name="EdgeRTarGz" label="EdgeR tar gz file" type="data" format="txt"/>
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21 <param name="TMM_Matrix_FPKM" label="TMM Normalized FPKM matrix" type="data" format="tabular" />
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22 <param name="Pvalue" label="P-value" value="0.05" type="float" />
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23 <param name="Cvalue" label="C-value" value="0" type="float" />
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24
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25 </inputs>
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26 <outputs>
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27 <data format="data" name="diffExpr_matrix" label="${tool.name} on ${on_string}: Matrix" from_work_dir="diffExpr.matrix"/>
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28 <data format="data" name="diffExpr_correlation_matrix" label="${tool.name} on ${on_string}: Sample_Correlation_Matrix" from_work_dir="diffExpr.matrix.log2.sample_cor.dat"/>
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29 <data format="data" name="diffExpr_correlation_matrix_pdf" label="${tool.name} on ${on_string}: Sample_Correlation_Matrix_PDF" from_work_dir="diffExpr.matrix.log2.sample_cor_matrix.pdf"/>
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30 <data format="data" name="Heatmap" label="${tool.name} on ${on_string}: Heatmap" from_work_dir="diffExpr.matrix.log2.centered.genes_vs_samples_heatmap.pdf"/>
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31 </outputs>
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32 <tests>
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33 <test>
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34 <param name="EdgeRTarGz" value="Sp.edgeR.tar.gz" ftype="tar" />
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35 <param name="TMM_Matrix_FPKM" value="Sp.TMM.EXPR.matrix" />
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36 <param name="Pvalue" value="0.05" />
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37 <param name="Cvalue" value="0.0" />
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38
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39 <output name="diffExpr_matrix" >
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40 <assert_contents>
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41 <has_line_matching expression=".+" />
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42 <has_line line="Sp_ds&#009;Sp_hs" />
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43 <has_line_matching expression="TRINITY_DN.+" />
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44 </assert_contents>
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45 </output>
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46 <output name="diffExpr_correlation_matrix" file="Sp.diffExpr.matrix.log2.sample_cor.dat" />
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47 <output name="diffExpr_correlation_matrix_pdf" >
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48 <assert_contents>
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49 <has_line_matching expression=".+" />
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50 </assert_contents>
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51 </output>
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52 <output name="Heatmap" >
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53 <assert_contents>
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54 <has_line_matching expression=".+" />
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55 </assert_contents>
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56 </output>
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57
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58 </test>
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59 </tests>
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60 <help>
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61 .. class:: infomark
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62
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63 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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64
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65 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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66
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67 .. _here: https://github.com/trinityrnaseq/GalaxyTrinityProtocol/wiki
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68 .. _paper: http://www.nature.com/nprot/journal/v8/n8/full/nprot.2013.084.html
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69 </help>
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70
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71 <citations>
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72 <citation type="doi">10.1038/nbt.1883</citation>
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73 </citations>
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74
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75 </tool>