comparison edgeR_Differential_Gene_Expression.xml @ 108:a02794bb9073 draft

planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty

107:049d8bc2214e

<?xml version="1.0" encoding="UTF-8"?>
<tool id="edger_dge" name="edgeR: Differential Gene(Expression) Analysis" version="3.11.0.a">
    <description>RNA-Seq gene expression analysis using edgeR (R package)</description>
    
    <requirements>
        <requirement type="package" version="3.11.0">edger</requirement>
    </requirements>
    
    <stdio>
        <regex match="Error in[^a-z]+contrasts"
                source="both"
                level="fatal"
                description="Have the design- and expression-matrix been swapped?" />
        <regex match="Execution halted"
                source="both"
                level="fatal" />
        <regex match="Calculating library sizes from column" 
                source="stderr" 
                level="log" />
        <regex match="During startup - Warning messages"
                source="stderr"
                level="log" />
        <regex match="Setting LC_[^ ]+ failed"
                source="stderr"
                level="warning"
                description="LOCALE has not been set correctly" />
    </stdio>
    
    <version_command>echo $(R --version | grep version | grep -v GNU) " , EdgeR version" $(R --vanilla --slave -e "library(edgeR) ; cat(sessionInfo()\$otherPkgs\$edgeR\$Version)" 2&gt; /dev/null | grep -v -i "WARNING: ")</version_command>
    
    <command>

------------

This tool requires no specific configurations. The following dependencies are installed automatically:

- R
- Bioconductor
    - limma
    - edgeR

License
-------
- R
    - GPL 2 & GPL 3

*Yuwen Liu, Jie Zhou and Kevin P. White* - Bioinformatics (2014) 30 (3): 301-304.

- http://www.ncbi.nlm.nih.gov/pubmed/24319002
- http://dx.doi.org/10.1093/bioinformatics/btt688

Contact
-------

The tool wrapper has been written by Youri Hoogstrate from the Erasmus
Medical Center (Rotterdam, Netherlands) on behalf of the Translational
Research IT (TraIT) project:

http://www.ctmm.nl/en/programmas/infrastructuren/traitprojecttranslationeleresearch

More tools by the Translational Research IT (TraIT) project can be found
in the following toolsheds:

http://toolshed.dtls.nl/

http://toolshed.g2.bx.psu.edu

http://testtoolshed.g2.bx.psu.edu/

I would like to thank Hina Riaz - Naz Khan for her helpful contribution.
    </help>
    
    <citations>
        <citation type="doi">10.1093/bioinformatics/btp616</citation>
        <citation type="doi">10.1093/bioinformatics/btt688</citation>
    </citations>
</tool>

108:a02794bb9073

<?xml version="1.0" encoding="UTF-8"?>
<tool id="edger_dge" name="edgeR: Differential Gene(Expression) Analysis" version="3.11.0.a">
    <description>RNA-Seq gene expression analysis using edgeR (R package)</description>
    
    <macros>
        <import>edgeR_macros.xml</import>
    </macros>
    
    <requirements>
        <requirement type="package" version="3.11.0">edger</requirement>
    </requirements>
    
    <stdio>
        <regex match="Error in[^a-z]+contrasts"
               source="both"
               level="fatal"
               description="Have the design- and expression-matrix been swapped?" />
        <regex match="Execution halted"
               source="both"
               level="fatal" />
        <regex match="Calculating library sizes from column" 
               source="stderr" 
               level="log" />
        <regex match="During startup - Warning messages"
               source="stderr"
               level="log" />
        <regex match="Setting LC_[^ ]+ failed"
               source="stderr"
               level="warning"
               description="LOCALE has not been set correctly" />
    </stdio>
    
    <version_command>echo $(R --version | grep version | grep -v GNU) " , EdgeR version" $(R --vanilla --slave -e "library(edgeR) ; cat(sessionInfo()\$otherPkgs\$edgeR\$Version)" 2&gt; /dev/null | grep -v -i "WARNING: ")</version_command>
    
    <command>

------------

This tool requires no specific configurations. The following dependencies are installed automatically:

- R
- limma
- edgeR

License
-------
- R
    - GPL 2 & GPL 3

*Yuwen Liu, Jie Zhou and Kevin P. White* - Bioinformatics (2014) 30 (3): 301-304.

- http://www.ncbi.nlm.nih.gov/pubmed/24319002
- http://dx.doi.org/10.1093/bioinformatics/btt688

@CONTACT@
    </help>
    
    <expand macro="citations" />
</tool>