|
0
|
1 <tool id="EdgeR_differentialExpression" name="EdgeR_differentialExpression" version="1.0.0">
|
|
|
2
|
|
|
3 <description>Identify Differentially Expressed Transcripts Using EdgeR</description>
|
|
|
4 <requirements>
|
|
|
5 <requirement type="package" version="2.7">python</requirement>
|
|
|
6 <requirement type="package">trinity</requirement>
|
|
|
7 </requirements>
|
|
|
8 <command>
|
|
|
9 <![CDATA[
|
|
|
10 python $__tool_directory__/EdgeR_differentialExpression_wrapper.py
|
|
|
11 $counts_matrix
|
|
|
12 $dispersion
|
|
|
13 ]]>
|
|
|
14 </command>
|
|
|
15 <inputs>
|
|
|
16
|
|
|
17 <param type="data" format="txt" name="counts_matrix" label="Matrix of RNA-Seq fragment counts for transcripts per condition" />
|
|
|
18 <param type="data" format="fasta" name="transcripts_fasta_file" label="Transcripts fasta file corresponding to matrix" />
|
|
|
19 <param type="float" name="dispersion" value="0.1" min="0" label="dispersion value" help="Dispersion value to be used in the negative binomial" />
|
|
|
20
|
|
|
21 </inputs>
|
|
|
22 <outputs>
|
|
1
|
23 <!--
|
|
0
|
24 <data format="tar.gz" name="EdgeR_Archive" label="${tool.name} on ${on_string}: EdgeR_Results.tar.gz" from_work_dir="edgeR_results.tar.gz" />
|
|
1
|
25 -->
|
|
2
|
26 <data format="txt" name="EdgeR_Archive" label="${tool.name} on ${on_string}: EdgeR_Results.tar.gz" from_work_dir="edgeR_results.tar.gz" />
|
|
0
|
27
|
|
|
28 </outputs>
|
|
|
29 <tests>
|
|
|
30 <test>
|
|
|
31 <param name="counts_matrix" value="Sp.counts.matrix" />
|
|
|
32 <!-- The transcripts_fasta_file does not seem to be used for anything. -->
|
|
|
33 <param name="transcripts_fasta_file" value="Sp.Trinity.fasta" />
|
|
|
34 <param name="dispersion" value="0.1" />
|
|
|
35
|
|
|
36 <!-- One could create more detailed tests if the output files were explicitly
|
|
|
37 saved rather than placed into an archive. We had a case where the archive
|
|
|
38 was being created, but it was missing one of the files, or one of the
|
|
|
39 files was empty. There is no easy way to look into the archive file to
|
|
|
40 test this.
|
|
|
41 -->
|
|
|
42 <output name="EdgeR_Archive" >
|
|
|
43 <assert_contents>
|
|
|
44 <has_line_matching expression=".+" />
|
|
|
45 <!-- The following is the magic number for all gzip files. -->
|
|
|
46 <has_text_matching expression="\x1F\x8B" />
|
|
|
47 </assert_contents>
|
|
|
48 </output>
|
|
|
49 </test>
|
|
|
50 </tests>
|
|
|
51 <help>
|
|
|
52 .. class:: infomark
|
|
|
53
|
|
|
54 edgeR is a Bioconductor package focusing on the analysis of digital gene expression data derived from RNA-Seq sequencing technologies.
|
|
|
55
|
|
|
56 To learn more about edgeR read their paper_, visit their website_ , or read this user_ guide_ .
|
|
|
57 If you are following the Trinity RNA-seq protocol please go here_ for a galaxy tool walk through or the Nature Protocols publication_ .
|
|
|
58
|
|
|
59 .. _paper: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2796818/
|
|
|
60 .. _publication: http://www.nature.com/nprot/journal/v8/n8/full/nprot.2013.084.html
|
|
|
61 .. _user: https://bioconductor.org/packages/devel/bioc/vignettes/edgeR/inst/doc/edgeRUsersGuide.pdf
|
|
|
62 .. _guide: https://bioconductor.org/packages/devel/bioc/vignettes/edgeR/inst/doc/edgeRUsersGuide.pdf
|
|
|
63 .. _website: http://bioinf.wehi.edu.au/edgeR/
|
|
|
64 .. _here: https://github.com/trinityrnaseq/GalaxyTrinityProtocol/wiki
|
|
|
65 </help>
|
|
|
66
|
|
|
67 <citations>
|
|
|
68 <citation type="doi">10.1038/nbt.1883</citation>
|
|
|
69 </citations>
|
|
|
70
|
|
|
71 </tool>
|
