comparison tools/venn_list/venn_list.xml @ 11:679b6323db03 draft

v0.1.0 now using matplotlib_venn instead of limma R package via rpy. Contribution from Frederic Sapet.

10:20d347feb882

<tool id="venn_list" name="Venn Diagram" version="0.0.11">
    <description>from lists</description>
    <requirements>
        <requirement type="package" version="1.0.1">galaxy_sequence_utils</requirement>
        <requirement type="package" version="1.0.3">rpy</requirement>
        <requirement type="package" version="3.25.3">limma</requirement>
        <requirement type="package" version="1.67">biopython</requirement>
    </requirements>
    <version_command>
python $__tool_directory__/venn_list.py --version
    </version_command>
    <command detect_errors="aggressive">

reads). You could then show the different mappings (and their overlaps)
as a Venn Diagram, and the outside count would be the unmapped reads.

**Citations**

The Venn Diagrams are drawn using Gordon Smyth's limma package from
R/Bioconductor, http://www.bioconductor.org/

The R library is called from Python via rpy, http://rpy.sourceforge.net/

If you use this Galaxy tool in work leading to a scientific publication please
cite:

Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013).
Galaxy tools and workflows for sequence analysis with applications
in molecular plant pathology. PeerJ 1:e167
http://dx.doi.org/10.7717/peerj.167

This tool uses Biopython to read and write SFF files, so you may also wish to
cite the Biopython application note (and Galaxy too of course):

Cock et al 2009. Biopython: freely available Python tools for computational
molecular biology and bioinformatics. Bioinformatics 25(11) 1422-3.
http://dx.doi.org/10.1093/bioinformatics/btp163 pmid:19304878.

    </help>
    <citations>
        <citation type="doi">10.7717/peerj.167</citation>
        <citation type="doi">10.1093/bioinformatics/15.5.356</citation>

11:679b6323db03

<tool id="venn_list" name="Venn Diagram" version="0.1.0">
    <description>from lists</description>
    <requirements>
        <requirement type="package" version="1.1.3">galaxy_sequence_utils</requirement>
        <requirement type="package" version="1.67">biopython</requirement>
        <requirement type="package" version="2.0.0">matplotlib</requirement>
        <requirement type="package" version="0.11.5">matplotlib-venn</requirement>
    </requirements>
    <version_command>
python $__tool_directory__/venn_list.py --version
    </version_command>
    <command detect_errors="aggressive">

reads). You could then show the different mappings (and their overlaps)
as a Venn Diagram, and the outside count would be the unmapped reads.

**Citations**

The Venn Diagrams are drawn using Konstantin Tretyakov's matplotlib-venn
package, https://pypi.org/project/matplotlib-venn/


If you use this Galaxy tool in work leading to a scientific publication please
cite:

Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013).
Galaxy tools and workflows for sequence analysis with applications
in molecular plant pathology. PeerJ 1:e167
https://doi.org/10.7717/peerj.167

This tool uses Biopython to read and write SFF files, so you may also wish to
cite the Biopython application note (and Galaxy too of course):

Cock et al 2009. Biopython: freely available Python tools for computational
molecular biology and bioinformatics. Bioinformatics 25(11) 1422-3.
https://doi.org/10.1093/bioinformatics/btp163 pmid:19304878.

    </help>
    <citations>
        <citation type="doi">10.7717/peerj.167</citation>
        <citation type="doi">10.1093/bioinformatics/15.5.356</citation>