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annotate ctat_edger_differential_expression.xml @ 0:f77032cd0463 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 10:42:33 -0400
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children 57907c40385c
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1 <tool id="ctat_edger_differential_expression" name="ctat_edger_differential_expression" version="1.0.0" profile="17.05">
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2
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3 <description>Identify Differentially Expressed Transcripts Using EdgeR</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_edger_differential_expression.py
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17 $counts_matrix
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18 $dispersion
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19 ]]>
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20 </command>
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21 <inputs>
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22
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23 <param type="data" format="txt" name="counts_matrix" label="Matrix of RNA-Seq fragment counts for transcripts per condition" />
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24 <param type="data" format="fasta" name="transcripts_fasta_file" label="Transcripts fasta file corresponding to matrix" />
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25 <param type="float" name="dispersion" value="0.1" min="0" label="dispersion value" help="Dispersion value to be used in the negative binomial" />
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26
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27 </inputs>
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28 <outputs>
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29 <!--
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30 <data format="tar.gz" name="EdgeR_Archive" label="${tool.name} on ${on_string}: EdgeR_Results.tar.gz" from_work_dir="edgeR_results.tar.gz" />
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31 -->
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32 <data format="txt" name="EdgeR_Archive" label="${tool.name} on ${on_string}: EdgeR_Results.tar.gz" from_work_dir="edgeR_results.tar.gz" />
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33
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34 </outputs>
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35 <tests>
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36 <test>
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37 <param name="counts_matrix" value="Sp.counts.matrix" />
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38 <!-- The transcripts_fasta_file does not seem to be used for anything. -->
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39 <param name="transcripts_fasta_file" value="Sp.Trinity.fasta" />
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40 <param name="dispersion" value="0.1" />
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41
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42 <!-- One could create more detailed tests if the output files were explicitly
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43 saved rather than placed into an archive. We had a case where the archive
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44 was being created, but it was missing one of the files, or one of the
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45 files was empty. There is no easy way to look into the archive file to
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46 test this.
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47 -->
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48 <output name="EdgeR_Archive" >
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49 <assert_contents>
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50 <has_line_matching expression=".+" />
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51 <!-- The following is the magic number for all gzip files. -->
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52 <has_text_matching expression="\x1F\x8B" />
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53 </assert_contents>
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54 </output>
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55 </test>
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56 </tests>
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57 <help>
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58 .. class:: infomark
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59
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60 edgeR is a Bioconductor package focusing on the analysis of digital gene expression data derived from RNA-Seq sequencing technologies.
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61
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62 To learn more about edgeR read their paper_, visit their website_ , or read this user_ guide_ .
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63 If you are following the Trinity RNA-seq protocol please go here_ for a galaxy tool walk through or the Nature Protocols publication_ .
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64
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65 .. _paper: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2796818/
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66 .. _publication: http://www.nature.com/nprot/journal/v8/n8/full/nprot.2013.084.html
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67 .. _user: https://bioconductor.org/packages/devel/bioc/vignettes/edgeR/inst/doc/edgeRUsersGuide.pdf
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68 .. _guide: https://bioconductor.org/packages/devel/bioc/vignettes/edgeR/inst/doc/edgeRUsersGuide.pdf
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69 .. _website: http://bioinf.wehi.edu.au/edgeR/
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70 .. _here: https://github.com/trinityrnaseq/GalaxyTrinityProtocol/wiki
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71 </help>
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72
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73 <citations>
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74 <citation type="doi">10.1038/nbt.1883</citation>
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75 </citations>
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76
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77 </tool>