view split_fasta.xml @ 0:3918528c19b4 draft

planemo upload

<tool id="statonlab_fasta_splitter" name="statonlab_fasta_splitter" version="1.0.0">
    <description>Split a single FASTA file into multiple smaller FASTA files&#xD;
    </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="5.22.2.1">perl</requirement>
    </requirements>
    <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__}/'split_fasta_render.R

	-o '$report'
	-d '$report.files_path'
	-s '$sink_message'
	-A '$fasta_input'
	-B '$number'
]]></command>
    <inputs>
        <param type="data" name="fasta_input" label="FASTA input" optional="False" multiple="False"/>
        <param type="integer" name="number" label="Number" help="The number of files the FASTA file will be split into"
               optional="False" value="200" min="1"/>
    </inputs>
    <outputs>
        <data format="html" name="report" label="tool report"/>
        <data format="txt" name="sink_message" label="Warnings and Errors" from_work_dir="warnings_and_errors.txt"/>
        <collection name="list_collection" type="list" label="${tool.name} on ${on_string}">
            <discover_datasets pattern="__name_and_ext__" directory="fasta_files" visible="true"/>
        </collection>
    </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>