Mercurial > repos > artbio > small_rna_signatures
changeset 10:68ee7c84d498 draft
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit 4e84386b619a7941f23d175d7fc86aba7990ac36"
| author | artbio |
|---|---|
| date | Tue, 07 Jan 2020 06:59:56 -0500 |
| parents | 59ee49bfb7bb |
| children | 8d3ca9652a5b |
| files | signature.xml |
| diffstat | 1 files changed, 5 insertions(+), 5 deletions(-) [+] |
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--- a/signature.xml Fri Apr 26 09:01:17 2019 -0400 +++ b/signature.xml Tue Jan 07 06:59:56 2020 -0500 @@ -1,4 +1,4 @@ -<tool id="signature" name="Small RNA Signatures" version="3.2.0"> +<tool id="signature" name="Small RNA Signatures" version="3.2.1"> <description /> <requirements> <requirement type="package" version="1.11.2=py27_0">numpy</requirement> @@ -89,7 +89,7 @@ Compute small RNA (piRNA, siRNA, ...) signatures. -This tool computes (i) the number of pairs **aligned** reads by overlap classes (in nt) and associated the z-scores, +This tool computes (i) the number of pairs **aligned** reads by overlap classes (in nt) and associated z-scores, and (ii) the ping-pong signal (`Brennecke et al, 2009`_) and associated z-scores. **Note** that the number of pairs of aligned reads is disctint from the number of pairs of reads @@ -97,7 +97,7 @@ when the analysis is restricted to uniquely mapping reads. Options set the min and max size of both the query small rna class and the target small rna class, -the range over which to compute the signatures, and whether the signatures should be reported at +the range of overlaps (in nt) over which to compute the signatures, and whether the signatures should be reported at genome-wide level or by item (chromosomes, genes, etc.). For details on computational algorithmes for piRNA and siRNA signatures, see `Antoniewski (2014)`_. @@ -110,10 +110,10 @@ **Outputs** -**Global**: The number of pairs founds, the ping-pong signal and the associated z-scores +**Global**: The number of pairs found, the ping-pong signal and the associated z-scores are computed at genome-wide level and returned in a pdf file. -**Lattice**: The number of pairs founds, the ping-pong signals and the associated z-scores +**Lattice**: The number of pairs found, the ping-pong signals and the associated z-scores are computed for each items described in the BAM alignment input and returned in a pdf file as a lattice graph.