annotate rseqc_macros.xml @ 49:6b33e31bda10 draft

Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2

<macros>

    <xml name="requirement_package_r"><requirement type="package" version="3.0.3">R</requirement></xml>
    <xml name="requirement_package_numpy"><requirement type="package" version="1.7.1">numpy</requirement></xml>
    <xml name="requirement_package_rseqc"><requirement type="package" version="2.4">rseqc</requirement></xml>

    <xml name="stdio">
        <stdio>
            <exit_code range="1:" level="fatal" description="An error occured during execution, see stderr and stdout for more information" />
            <regex match="[Ee]rror" source="both" description="An error occured during execution, see stderr and stdout for more information" />
        </stdio>
    </xml>

    <xml name="citations">
        <citations>
            <citation type="bibtex">
    @article{wang_rseqc:_2012,
        title = {{RSeQC}: quality control of {RNA}-seq experiments},
        volume = {28},
        issn = {1367-4803, 1460-2059},
        shorttitle = {{RSeQC}},
        url = {http://bioinformatics.oxfordjournals.org/content/28/16/2184},
        doi = {10.1093/bioinformatics/bts356},
        abstract = {Motivation: RNA-seq has been extensively used for transcriptome study. Quality control (QC) is critical to ensure that RNA-seq data are of high quality and suitable for subsequent analyses. However, QC is a time-consuming and complex task, due to the massive size and versatile nature of RNA-seq data. Therefore, a convenient and comprehensive QC tool to assess RNA-seq quality is sorely needed.
    Results: We developed the RSeQC package to comprehensively evaluate different aspects of RNA-seq experiments, such as sequence quality, GC bias, polymerase chain reaction bias, nucleotide composition bias, sequencing depth, strand specificity, coverage uniformity and read distribution over the genome structure. RSeQC takes both SAM and BAM files as input, which can be produced by most RNA-seq mapping tools as well as BED files, which are widely used for gene models. Most modules in RSeQC take advantage of R scripts for visualization, and they are notably efficient in dealing with large BAM/SAM files containing hundreds of millions of alignments.
    Availability and implementation: RSeQC is written in Python and C. Source code and a comprehensive user's manual are freely available at: http://code.google.com/p/rseqc/.
    Contact: WL1\{at\}bcm.edu
    Supplementary Information: Supplementary data are available at Bioinformatics online.},
        language = {en},
        number = {16},
        urldate = {2015-06-30},
        journal = {Bioinformatics},
        author = {Wang, Liguo and Wang, Shengqin and Li, Wei},
        month = aug,
        year = {2012},
        pmid = {22743226},
        pages = {2184--2185},
    }
            </citation>
        </citations>
    </xml>
</macros>