comparison signature.xml @ 7:07771982ef9b draft

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit 7276b6b73aef7af4058ad2c1e34c4557e9cccbe0

6:4da23f009c9e

<tool id="signature" name="Small RNA Signatures" version="3.0.0">
    <description />
    <requirements>
        <requirement type="package" version="1.11.2=py27_0">numpy</requirement>
        <requirement type="package" version="0.11.2.1=py27_0">pysam</requirement>
        <requirement type="package" version="1.3.2=r3.3.1_0">r-optparse</requirement>

**What it does**

Compute small RNA (piRNA, siRNA, ...) signatures.

This tool computes (i) the number of pairs by overlap classes (in nt) and associated the z-scores,
and (ii) the ping-pong signal (`Brennecke et al, 2009`_) and associated z-scores. 
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 
genome-wide level or by item (chromosomes, genes, etc.). For details on computational algorithmes 
for piRNA and siRNA signatures, see `Antoniewski (2014)`_.

7:07771982ef9b

<tool id="signature" name="Small RNA Signatures" version="3.1.0">
    <description />
    <requirements>
        <requirement type="package" version="1.11.2=py27_0">numpy</requirement>
        <requirement type="package" version="0.11.2.1=py27_0">pysam</requirement>
        <requirement type="package" version="1.3.2=r3.3.1_0">r-optparse</requirement>

**What it does**

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,
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
when these reads can be aligned at multiple positions in the genome. The two values are equal only
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 
genome-wide level or by item (chromosomes, genes, etc.). For details on computational algorithmes 
for piRNA and siRNA signatures, see `Antoniewski (2014)`_.