Mercurial > repos > mingchen0919 > elastic_sra_toolkit

<macros>

    <!--change tool_id and elastic tool in the first line of elastic_tool.xml with appropriate tool_id and tool_name.-->

    <!--add tool requirements-->
    <xml name="tool_requirements">
        <requirement type="package" version="1.15.0.6-0">pandoc</requirement>
        <requirement type="package" version="1.6">r-rmarkdown</requirement>
        <requirement type="package" version="2.8.2">sra-tools</requirement>
    </xml>

    <!--add tool description-->
    <xml name="tool_description">
        <description>a collection of tools and libraries for using data in the INSDC Sequence Read Archives.</description>
    </xml>

    <!--add tool options-->
    <xml name="tool_options">
        <option value="fastq-dump" selected="true">fastq-dump</option>
        <option value="prefetch" selected="false">prefetch</option>
        <option value="sam-dump" selected="false">sam-dump</option>
        <option value="sra-pileup" selected="false">sra-pileup</option>
        <option value="vdb-config" selected="false">vdb-config</option>
        <option value="vdb-decrypt" selected="false">vdb-decrypt</option>
        <option value="abi-dump" selected="false">abi-dump</option>
        <option value="illumina-dump" selected="false">illumina-dump</option>
        <option value="sff-dump" selected="false">sff-dump</option>
        <option value="sra-stat" selected="false">sra-stat</option>
        <option value="vdb-dump" selected="false">vdb-dump</option>
        <option value="vdb-encrypt" selected="false">vdb-encrypt</option>
        <option value="vdb-validate" selected="false">vdb-validate</option>
    </xml>

    <!--add tool help-->
    <xml name="tool_help">
        <help><![CDATA[
            [SRA Toolkit Documentation](http://ncbi.github.io/sra-tools/)

            Example 1: download paired end reads and split them into forward and reverse reads.
              Tool name: fastq-dump
              + 1: PATH: relative to this tool output directory
                  * option: -O
                  * value: SRA
                  * path type: directory path
              + 1: INPUT VALUE: string/float/integer
                  * option: --split-files
                  * value: SRR6077558 ERR343809

            Example 2: download single end reads
              Tool name: fastq-dump
              + 1: PATH: relative to this tool output directory
                  * option: -O
                  * value: SRA
                  * path type: directory path
              + 1: INPUT VALUE: string/float/integer
                  * value: SRR6077558 ERR343809
        ]]></help>
    </xml>

    <!--add tool citations-->
    <xml name="citations">
        <citation type="bibtex"><![CDATA[
            @article{allaire2016rmarkdown,
            title={rmarkdown: Dynamic Documents for R, 2016},
            author={Allaire, J and Cheng, Joe and Xie, Yihui and McPherson, Jonathan and Chang, Winston and Allen, Jeff
            and Wickham, Hadley and Atkins, Aron and Hyndman, Rob},
            journal={R package version 0.9},
            volume={6},
            year={2016}
            }
        ]]></citation>
        <citation type="bibtex"><![CDATA[
            @book{xie2015elastic,
            title={Dynamic Documents with R and knitr},
            author={Xie, Yihui},
            volume={29},
            year={2015},
            publisher={CRC Press}
            }
        ]]></citation>
    </xml>
</macros>
author	mingchen0919
date	Sun, 01 Apr 2018 23:45:00 -0400
parents	6259ffa3d2d3
children