view interproscan.xml @ 5:4aa0cec3399f draft default tip

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<tool id="statonlab_interproscan" name="statonlab interproscan" version="1.0.0">
    <description>search nucleotide and protein sequences</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>
    </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__}/'interproscan_render.R

	-o '$report'
	-d '$report.files_path'
	-s '$sink_message'
	-A '$fasta_input'
	-B '$output_format'
	-C '$disable_precalc'
	-D '$iprlookup'
	-E '$goterms'
	-F '$pathways'
]]></command>
    <inputs>
        <param type="data" name="fasta_input" label="sequences in fasta format" optional="False" format="fasta,fa"/>
        <param type="select" name="output_format" argument="-f" label="Output format" optional="False" multiple="True">
            <option value="TSV" selected="false">TSV</option>
            <option value="XML" selected="false">XML</option>
            <option value="JSON" selected="false">JSON</option>
            <option value="GFF3" selected="false">GFF3</option>
            <option value="HTML" selected="false">HTML</option>
            <option value="SVG" selected="false">SVG</option>
        </param>
        <param type="boolean" name="disable_precalc" argument="--disable-precalc" label="disable precalc"
               help="Disables use of the precalculated match lookup service" optional="False" checked="True"
               truevalue="NO_ARGUMENT_YES" falsevalue="NO_ARGUMENT_NO"/>
        <param type="boolean" name="iprlookup" argument="--iprlookup" label="lookup corresponding InterPro annotation"
               help="Also include lookup of corresponding InterPro annotation in the TSV and GFF3 output formats"
               optional="False" checked="True" truevalue="NO_ARGUMENT_YES" falsevalue="NO_ARGUMENT_NO"/>
        <param type="boolean" name="goterms" argument="--goterms"
               label="switch on lookup of corresponding Gene Ontology" optional="False" checked="True"
               truevalue="NO_ARGUMENT_YES" falsevalue="NO_ARGUMENT_NO"/>
        <param type="boolean" name="pathways" argument="--pathways"
               label="switch on lookup of corresponding Pathway annotation" optional="False" checked="True"
               truevalue="NO_ARGUMENT_YES" falsevalue="NO_ARGUMENT_NO"/>
    </inputs>
    <outputs>
        <data name="report" format="html" label="${tool.name} on ${on_string}" hidden="false"/>
        <data name="sink_message" format="txt" label="${tool.name} log on ${on_string}"
              from_work_dir="warnings_and_errors.txt" hidden="false"/>
    </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>
        <citation type="bibtex"><![CDATA[@article{jones2014interproscan,
  title={InterProScan 5: genome-scale protein function classification},
  author={Jones, Philip and Binns, David and Chang, Hsin-Yu and Fraser, Matthew and Li, Weizhong and McAnulla, Craig and McWilliam, Hamish and Maslen, John and Mitchell, Alex and Nuka, Gift and others},
  journal={Bioinformatics},
  volume={30},
  number={9},
  pages={1236--1240},
  year={2014},
  publisher={Oxford University Press}
}]]></citation>
    </citations>
</tool>