comparison signature.xml @ 12:aa5e2c64dff8 draft

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit 6806c0677e53d52164707faeb36947987f5c500a

11:8d3ca9652a5b

<tool id="signature" name="Small RNA Signatures" version="3.3>">
    <description />
    <requirements>
        <requirement type="package" version="1.13=h8c37831_0">samtools</requirement>
        <requirement type="package" version="1.21.3=py37h31617e3_0">numpy</requirement>
        <requirement type="package" version="0.16.0.1=py37h45aed0b_3">pysam</requirement>
        <requirement type="package" version="1.7.1=r40hc72bb7e_0">r-optparse</requirement>
        <requirement type="package" version="0.6_29=r40hc72bb7e_1">r-latticeextra</requirement>
        <requirement type="package" version="2.3=r40hc72bb7e_1003">r-gridextra</requirement>
    </requirements>
    <stdio>
        <exit_code range="1:" level="fatal" description="Tool exception" />
    </stdio>
      <command detect_errors="exit_code"><![CDATA[
        samtools index '$input' &&
        python '$__tool_directory__'/signature.py
           --input '$input'
           --minquery '$minquery'
           --maxquery '$maxquery'
           --mintarget '$mintarget'
           --maxtarget '$maxtarget'
           --minscope '$minscope'

**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

**Input**

A **sorted** BAM alignment file.

12:aa5e2c64dff8

<tool id="signature" name="Small RNA Signatures" version="3.4.1>">
    <description />
    <requirements>
        <requirement type="package" version="1.23.4">numpy</requirement>
        <requirement type="package" version="0.18.0">pysam</requirement>
        <requirement type="package" version="1.7.3">r-optparse</requirement>
        <requirement type="package" version="0.6_30">r-latticeextra</requirement>
        <requirement type="package" version="2.3">r-gridextra</requirement>
    </requirements>
    <stdio>
        <exit_code range="1:" level="fatal" description="Tool exception" />
    </stdio>
      <command detect_errors="exit_code"><![CDATA[
        ln -f -s $input.metadata.bam_index input.bam.bai &&
        ln -s $input input.bam &&
        python '$__tool_directory__'/signature.py
           --input input.bam
           --minquery '$minquery'
           --maxquery '$maxquery'
           --mintarget '$mintarget'
           --maxtarget '$maxtarget'
           --minscope '$minscope'

**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. Science. 2008;322: 1387–1392) 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)`_.

.. _Antoniewski (2014): https://link.springer.com/protocol/10.1007%2F978-1-4939-0931-5_12

**Input**

A **sorted** BAM alignment file.