annotate cuffdata_cummerbund.xml @ 0:da7241f92ecf

Uploaded
author jjohnson
date Mon, 04 Feb 2013 19:50:25 -0500
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
1 <tool id="cuffdata_cummerbund" name="Cuffdata cummeRbund DB" version="0.0.5">
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
2 <!-- Wrapper supports Cuffdiff versions v1.3.0-v2.0 -->
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
3 <description>Create CummeRbund database</description>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
4 <command>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
5 ## symlink all files to job working dir
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
6 for i in ${cuffdata.extra_files_path}/*; #raw do ln -s $i ${i##*/}; done; #end raw
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
7 ## run rscript
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
8 Rscript --vanilla --quiet -e 'library(cummeRbund); cuff&lt;-readCufflinks(dbFile="cuffData.db"); samples(cuff@genes); cuff' 2> r.stderr | sed 's/\[1\]/samples:/'
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
9 </command>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
10 <inputs>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
11 <param name="cuffdata" type="data" format="cuffdata" label="Cuffidif cuffdata" help=""/>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
12 </inputs>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
13
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
14 <outputs>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
15 <data format="cuffdatadb" name="cummeRbund_db" label="${tool.name} on ${on_string}: cummeRbund sqlite Database" from_work_dir="cuffData.db"/>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
16 </outputs>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
17 <stdio>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
18 <exit_code range="1:" level="fatal" description="Cufflinks Err" />
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
19 </stdio>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
20 <tests>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
21 </tests>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
22 <help>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
23 **Cuffdiff cuffdata to CummeRBund database**
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
24
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
25 Create a CummeRBund_ SQLite database from the cuffdata output from Cuffdiff_.
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
26
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
27 Cuffdiff_ is part of Cufflinks_. Cuffdiff find significant changes in transcript expression, splicing, and promoter use. Please cite: Trapnell C, Williams BA, Pertea G, Mortazavi AM, Kwan G, van Baren MJ, Salzberg SL, Wold B, Pachter L. Transcript assembly and abundance estimation from RNA-Seq reveals thousands of new transcripts and switching among isoforms. Nature Biotechnology doi:10.1038/nbt.1621
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
28
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
29 CummeRbund_ is a collaborative effort between the Computational Biology group led by Manolis Kellis at MIT's Computer Science and Artificial Intelligence Laboratory, and the Rinn Lab at the Harvard University department of Stem Cells and Regenerative Medicine
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
30
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
31 .. _CummeRBund: http://compbio.mit.edu/cummeRbund/
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
32 .. _Cufflinks: http://cufflinks.cbcb.umd.edu/
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
33 .. _Cuffdiff: http://cufflinks.cbcb.umd.edu/manual.html#cuffdiff
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
34
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
35 </help>
da7241f92ecf Uploaded
jjohnson
parents:
diff changeset
36 </tool>