Mercurial > repos > trinity_ctat > ctat_edger_differential_expression

annotate ctat_edger_differential_expression.xml @ 1:57907c40385c draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Updating tools requirements.
author trinity_ctat
date Wed, 27 Jun 2018 14:12:38 -0400
parents f77032cd0463
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
f77032cd0463 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool.
trinity_ctat
parents:
diff changeset
1 <tool id="ctat_edger_differential_expression" name="ctat_edger_differential_expression" version="1.0.0" profile="17.05">
f77032cd0463 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool.
trinity_ctat
parents:
diff changeset
2
f77032cd0463 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool.
trinity_ctat
parents:
diff changeset
3 <description>Identify Differentially Expressed Transcripts Using EdgeR</description>
f77032cd0463 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool.
trinity_ctat
parents:
diff changeset
4 <requirements>
f77032cd0463 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool.
trinity_ctat
parents:
diff changeset
5 <requirement type="package" version="2.7">python</requirement>
f77032cd0463 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool.
trinity_ctat
parents:
diff changeset
6 <requirement type="package">subprocess32</requirement>
f77032cd0463 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool.
trinity_ctat
parents:
diff changeset
7 <requirement type="package">bzip2</requirement>
f77032cd0463 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool.
trinity_ctat
parents:
diff changeset
8 <requirement type="package" version="1.3.0">rsem</requirement>
f77032cd0463 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool.
trinity_ctat
parents:
diff changeset
9 <requirement type="package" version="3">bioconductor-edger</requirement>
f77032cd0463 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool.
trinity_ctat
parents:
diff changeset
10 <requirement type="package" version="2">bioconductor-qvalue</requirement>
1
57907c40385c Updating tools requirements.
trinity_ctat
parents: 0
diff changeset
11 <requirement type="package" version="2.6.6">trinity</requirement>
0
f77032cd0463 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool.
trinity_ctat
parents:
diff changeset
12 </requirements>
f77032cd0463 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool.
trinity_ctat
parents:
diff changeset
13 <command detect_errors="exit_code">
f77032cd0463 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool.
trinity_ctat
parents:
diff changeset
14 <![CDATA[
f77032cd0463 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool.
trinity_ctat
parents:
diff changeset
15 python $__tool_directory__/ctat_edger_differential_expression.py
f77032cd0463 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool.
trinity_ctat
parents:
diff changeset
16 $counts_matrix
f77032cd0463 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool.
trinity_ctat
parents:
diff changeset
17 $dispersion
f77032cd0463 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool.
trinity_ctat
parents:
diff changeset
18 ]]>
f77032cd0463 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool.
trinity_ctat
parents:
diff changeset
19 </command>
f77032cd0463 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool.
trinity_ctat
parents:
diff changeset
20 <inputs>
f77032cd0463 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool.
trinity_ctat
parents:
diff changeset
21
f77032cd0463 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool.
trinity_ctat
parents:
diff changeset
22 <param type="data" format="txt" name="counts_matrix" label="Matrix of RNA-Seq fragment counts for transcripts per condition" />
f77032cd0463 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool.
trinity_ctat
parents:
diff changeset
23 <param type="data" format="fasta" name="transcripts_fasta_file" label="Transcripts fasta file corresponding to matrix" />
f77032cd0463 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool.
trinity_ctat
parents:
diff changeset
24 <param type="float" name="dispersion" value="0.1" min="0" label="dispersion value" help="Dispersion value to be used in the negative binomial" />
f77032cd0463 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool.
trinity_ctat
parents:
diff changeset
25
f77032cd0463 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool.
trinity_ctat
parents:
diff changeset
26 </inputs>
f77032cd0463 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool.
trinity_ctat
parents:
diff changeset
27 <outputs>
f77032cd0463 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool.
trinity_ctat
parents:
diff changeset
28 <!--
f77032cd0463 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool.
trinity_ctat
parents:
diff changeset
29 <data format="tar.gz" name="EdgeR_Archive" label="${tool.name} on ${on_string}: EdgeR_Results.tar.gz" from_work_dir="edgeR_results.tar.gz" />
f77032cd0463 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool.
trinity_ctat
parents:
diff changeset
30 -->
f77032cd0463 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool.
trinity_ctat
parents:
diff changeset
31 <data format="txt" name="EdgeR_Archive" label="${tool.name} on ${on_string}: EdgeR_Results.tar.gz" from_work_dir="edgeR_results.tar.gz" />
f77032cd0463 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool.
trinity_ctat
parents:
diff changeset
32
f77032cd0463 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool.
trinity_ctat
parents:
diff changeset
33 </outputs>
f77032cd0463 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool.
trinity_ctat
parents:
diff changeset
34 <tests>
f77032cd0463 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool.
trinity_ctat
parents:
diff changeset
35 <test>
f77032cd0463 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool.
trinity_ctat
parents:
diff changeset
36 <param name="counts_matrix" value="Sp.counts.matrix" />
f77032cd0463 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool.
trinity_ctat
parents:
diff changeset
37 <!-- The transcripts_fasta_file does not seem to be used for anything. -->
f77032cd0463 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool.
trinity_ctat
parents:
diff changeset
38 <param name="transcripts_fasta_file" value="Sp.Trinity.fasta" />
f77032cd0463 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool.
trinity_ctat
parents:
diff changeset
39 <param name="dispersion" value="0.1" />
f77032cd0463 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool.
trinity_ctat
parents:
diff changeset
40
f77032cd0463 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool.
trinity_ctat
parents:
diff changeset
41 <!-- One could create more detailed tests if the output files were explicitly
f77032cd0463 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool.
trinity_ctat
parents:
diff changeset
42 saved rather than placed into an archive. We had a case where the archive
f77032cd0463 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool.
trinity_ctat
parents:
diff changeset
43 was being created, but it was missing one of the files, or one of the
f77032cd0463 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool.
trinity_ctat
parents:
diff changeset
44 files was empty. There is no easy way to look into the archive file to
f77032cd0463 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool.
trinity_ctat
parents:
diff changeset
45 test this.
f77032cd0463 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool.
trinity_ctat
parents:
diff changeset
46 -->
f77032cd0463 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool.
trinity_ctat
parents:
diff changeset
47 <output name="EdgeR_Archive" >
f77032cd0463 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool.
trinity_ctat
parents:
diff changeset
48 <assert_contents>
f77032cd0463 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool.
trinity_ctat
parents:
diff changeset
49 <has_line_matching expression=".+" />
f77032cd0463 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool.
trinity_ctat
parents:
diff changeset
50 <!-- The following is the magic number for all gzip files. -->
f77032cd0463 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool.
trinity_ctat
parents:
diff changeset
51 <has_text_matching expression="\x1F\x8B" />
f77032cd0463 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool.
trinity_ctat
parents:
diff changeset
52 </assert_contents>
f77032cd0463 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool.
trinity_ctat
parents:
diff changeset
53 </output>
f77032cd0463 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool.
trinity_ctat
parents:
diff changeset
54 </test>
f77032cd0463 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool.
trinity_ctat
parents:
diff changeset
55 </tests>
f77032cd0463 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool.
trinity_ctat
parents:
diff changeset
56 <help>
f77032cd0463 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool.
trinity_ctat
parents:
diff changeset
57 .. class:: infomark
f77032cd0463 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool.
trinity_ctat
parents:
diff changeset
58
f77032cd0463 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool.
trinity_ctat
parents:
diff changeset
59 edgeR is a Bioconductor package focusing on the analysis of digital gene expression data derived from RNA-Seq sequencing technologies.
f77032cd0463 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool.
trinity_ctat
parents:
diff changeset
60
f77032cd0463 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool.
trinity_ctat
parents:
diff changeset
61 To learn more about edgeR read their paper_, visit their website_ , or read this user_ guide_ .
f77032cd0463 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool.
trinity_ctat
parents:
diff changeset
62 If you are following the Trinity RNA-seq protocol please go here_ for a galaxy tool walk through or the Nature Protocols publication_ .
f77032cd0463 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool.
trinity_ctat
parents:
diff changeset
63
f77032cd0463 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool.
trinity_ctat
parents:
diff changeset
64 .. _paper: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2796818/
f77032cd0463 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool.
trinity_ctat
parents:
diff changeset
65 .. _publication: http://www.nature.com/nprot/journal/v8/n8/full/nprot.2013.084.html
f77032cd0463 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool.
trinity_ctat
parents:
diff changeset
66 .. _user: https://bioconductor.org/packages/devel/bioc/vignettes/edgeR/inst/doc/edgeRUsersGuide.pdf
f77032cd0463 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool.
trinity_ctat
parents:
diff changeset
67 .. _guide: https://bioconductor.org/packages/devel/bioc/vignettes/edgeR/inst/doc/edgeRUsersGuide.pdf
f77032cd0463 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool.
trinity_ctat
parents:
diff changeset
68 .. _website: http://bioinf.wehi.edu.au/edgeR/
f77032cd0463 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool.
trinity_ctat
parents:
diff changeset
69 .. _here: https://github.com/trinityrnaseq/GalaxyTrinityProtocol/wiki
f77032cd0463 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool.
trinity_ctat
parents:
diff changeset
70 </help>
f77032cd0463 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool.
trinity_ctat
parents:
diff changeset
71
f77032cd0463 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool.
trinity_ctat
parents:
diff changeset
72 <citations>
f77032cd0463 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool.
trinity_ctat
parents:
diff changeset
73 <citation type="doi">10.1038/nbt.1883</citation>
f77032cd0463 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool.
trinity_ctat
parents:
diff changeset
74 </citations>
f77032cd0463 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool.
trinity_ctat
parents:
diff changeset
75
f77032cd0463 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool.
trinity_ctat
parents:
diff changeset
76 </tool>