Mercurial > repos > trinity_ctat > edger_differential_expression
annotate EdgeR_differentialExpression.xml @ 5:d66c05101513 draft default tip
Adding profile info and exit code behavior. Making version numbers consistent. Upping test number.
| author | trinity_ctat |
|---|---|
| date | Fri, 06 Oct 2017 10:57:25 -0400 |
| parents | bfd09008aae7 |
| children |
| rev | line source |
|---|---|
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5
d66c05101513
Adding profile info and exit code behavior. Making version numbers consistent. Upping test number.
trinity_ctat
parents:
4
diff
changeset
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1 <tool id="EdgeR_differentialExpression" name="EdgeR_differentialExpression" version="1.0.0" profile="17.05"> |
| 0 | 2 |
| 3 <description>Identify Differentially Expressed Transcripts Using EdgeR</description> | |
| 4 <requirements> | |
| 5 <requirement type="package" version="2.7">python</requirement> | |
| 4 | 6 <requirement type="package" version="1.3.0">rsem</requirement> |
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5
d66c05101513
Adding profile info and exit code behavior. Making version numbers consistent. Upping test number.
trinity_ctat
parents:
4
diff
changeset
|
7 <requirement type="package" version="3">bioconductor-edger</requirement> |
| 0 | 8 <requirement type="package">trinity</requirement> |
| 9 </requirements> | |
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5
d66c05101513
Adding profile info and exit code behavior. Making version numbers consistent. Upping test number.
trinity_ctat
parents:
4
diff
changeset
|
10 <command detect_errors="exit_code"> |
| 0 | 11 <![CDATA[ |
| 12 python $__tool_directory__/EdgeR_differentialExpression_wrapper.py | |
| 13 $counts_matrix | |
| 14 $dispersion | |
| 15 ]]> | |
| 16 </command> | |
| 17 <inputs> | |
| 18 | |
| 19 <param type="data" format="txt" name="counts_matrix" label="Matrix of RNA-Seq fragment counts for transcripts per condition" /> | |
| 20 <param type="data" format="fasta" name="transcripts_fasta_file" label="Transcripts fasta file corresponding to matrix" /> | |
| 21 <param type="float" name="dispersion" value="0.1" min="0" label="dispersion value" help="Dispersion value to be used in the negative binomial" /> | |
| 22 | |
| 23 </inputs> | |
| 24 <outputs> | |
| 1 | 25 <!-- |
| 0 | 26 <data format="tar.gz" name="EdgeR_Archive" label="${tool.name} on ${on_string}: EdgeR_Results.tar.gz" from_work_dir="edgeR_results.tar.gz" /> |
| 1 | 27 --> |
| 2 | 28 <data format="txt" name="EdgeR_Archive" label="${tool.name} on ${on_string}: EdgeR_Results.tar.gz" from_work_dir="edgeR_results.tar.gz" /> |
| 0 | 29 |
| 30 </outputs> | |
| 31 <tests> | |
| 32 <test> | |
| 33 <param name="counts_matrix" value="Sp.counts.matrix" /> | |
| 34 <!-- The transcripts_fasta_file does not seem to be used for anything. --> | |
| 35 <param name="transcripts_fasta_file" value="Sp.Trinity.fasta" /> | |
| 36 <param name="dispersion" value="0.1" /> | |
| 37 | |
| 38 <!-- One could create more detailed tests if the output files were explicitly | |
| 39 saved rather than placed into an archive. We had a case where the archive | |
| 40 was being created, but it was missing one of the files, or one of the | |
| 41 files was empty. There is no easy way to look into the archive file to | |
| 42 test this. | |
| 43 --> | |
| 44 <output name="EdgeR_Archive" > | |
| 45 <assert_contents> | |
| 46 <has_line_matching expression=".+" /> | |
| 47 <!-- The following is the magic number for all gzip files. --> | |
| 48 <has_text_matching expression="\x1F\x8B" /> | |
| 49 </assert_contents> | |
| 50 </output> | |
| 51 </test> | |
| 52 </tests> | |
| 53 <help> | |
| 54 .. class:: infomark | |
| 55 | |
| 56 edgeR is a Bioconductor package focusing on the analysis of digital gene expression data derived from RNA-Seq sequencing technologies. | |
| 57 | |
| 58 To learn more about edgeR read their paper_, visit their website_ , or read this user_ guide_ . | |
| 59 If you are following the Trinity RNA-seq protocol please go here_ for a galaxy tool walk through or the Nature Protocols publication_ . | |
| 60 | |
| 61 .. _paper: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2796818/ | |
| 62 .. _publication: http://www.nature.com/nprot/journal/v8/n8/full/nprot.2013.084.html | |
| 63 .. _user: https://bioconductor.org/packages/devel/bioc/vignettes/edgeR/inst/doc/edgeRUsersGuide.pdf | |
| 64 .. _guide: https://bioconductor.org/packages/devel/bioc/vignettes/edgeR/inst/doc/edgeRUsersGuide.pdf | |
| 65 .. _website: http://bioinf.wehi.edu.au/edgeR/ | |
| 66 .. _here: https://github.com/trinityrnaseq/GalaxyTrinityProtocol/wiki | |
| 67 </help> | |
| 68 | |
| 69 <citations> | |
| 70 <citation type="doi">10.1038/nbt.1883</citation> | |
| 71 </citations> | |
| 72 | |
| 73 </tool> |