comparison signature.xml @ 10:68ee7c84d498 draft

"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit 4e84386b619a7941f23d175d7fc86aba7990ac36"

9:59ee49bfb7bb

<tool id="signature" name="Small RNA Signatures" version="3.2.0">
    <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="1.6.1=r351h6115d3f_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)`_.

.. _Brennecke et al, 2009: http://dx.doi.org/10.1126/science.1165171
.. _Antoniewski (2014): https://link.springer.com/protocol/10.1007%2F978-1-4939-0931-5_12

A **sorted** BAM alignment file.

**Outputs**

**Global**: The number of pairs founds, 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 
are computed for each items described in the BAM alignment input and returned in a pdf file as a lattice graph.


        </help>
    <citations>

10:68ee7c84d498

<tool id="signature" name="Small RNA Signatures" version="3.2.1">
    <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="1.6.1=r351h6115d3f_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 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 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)`_.

.. _Brennecke et al, 2009: http://dx.doi.org/10.1126/science.1165171
.. _Antoniewski (2014): https://link.springer.com/protocol/10.1007%2F978-1-4939-0931-5_12

A **sorted** BAM alignment file.

**Outputs**

**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 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.


        </help>
    <citations>