Mercurial > repos > mingchen0919 > mygene_and_myvariant

view variant_simple_search.xml @ 5:3a564664e40f draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
add advanced search
author mingchen0919
date Wed, 21 Mar 2018 08:54:18 -0400
parents 238ab20dc431
children
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<tool id="variant_simple_search" name="variant: ids search" version="1.0.0">
    <description>
        some description
    </description>
    <requirements>
        <requirement type="package" version="1.15.0.6-0">pandoc</requirement>
        <requirement type="package" version="1.20.0">r-getopt</requirement>
        <requirement type="package" version="1.6">r-rmarkdown</requirement>
        <requirement type="package" version="1.5">r-jsonlite</requirement>
        <requirement type="package" version="0.2">r-dt</requirement>
        <requirement type="package" version="3.1">r-curl</requirement>
        <requirement type="package" version="1.95_4.8">r-rcurl</requirement>
        <requirement type="package" version="1.3.1">r-httr</requirement>
    </requirements>
    <macros>
        <import>mygene_and_myvariant_macros.xml</import>
    </macros>
    <stdio>
        <regex match="XXX" source="stderr" level="warning"
               description="Check the warnings_and_errors.txt file for more details."/>
    </stdio>
    <command><![CDATA[
        export TOOL_DIR='${__tool_directory__}' &&

        Rscript '${__tool_directory__}/variant_simple_search_render.R'

			-o '$report'
			-d '$report.files_path'
			-s '$sink_message'
			-q '$variant_query'
			-f '$return_fields'


        
    ]]></command>
    <inputs>
        <param type="text" name="variant_query" label="Search keywords" optional="False">
            <sanitizer>
                <valid initial="string.printable"/>
            </sanitizer>
        </param>
        <param type="select" name="return_fields" label="Returned fields" optional="False" multiple="True">
            <option value="all">ALL_FIELDS</option>
            <expand macro="fields"/>
        </param>
    </inputs>
    <outputs>
        <data format="html" name="report" label="${tool.name} report"/>
        <data format="txt" name="sink_message" label="${tool.name} log" from_work_dir="warnings_and_errors.txt"/>
    </outputs>
    <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{xie2015dynamic,
            title={Dynamic Documents with R and knitr},
            author={Xie, Yihui},
            volume={29},
            year={2015},
            publisher={CRC Press}
            }
        ]]></citation>
    </citations>
</tool>