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0
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1 <tool id="statonlab_interproscan" name="statonlab interproscan" version="1.0.0">
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2 <description>search nucleotide and protein sequences</description>
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3 <requirements>
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4 <requirement type="package" version="1.15.0.6-0">pandoc</requirement>
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5 <requirement type="package" version="1.20.0">r-getopt</requirement>
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6 <requirement type="package" version="1.6">r-rmarkdown</requirement>
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7 </requirements>
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8 <stdio>
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9 <regex match="XXX" source="stderr" level="warning"
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10 description="Check the warnings_and_errors.txt file for more details."/>
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11 </stdio>
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12 <command><![CDATA[export TOOL_DIR='${__tool_directory__}' &&
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13
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14 Rscript '${__tool_directory__}/'interproscan_render.R
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15
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16 -o '$report'
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17 -d '$report.files_path'
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18 -s '$sink_message'
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19 -A '$fasta_input'
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20 -B '$output_format'
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21 -C '$disable_precalc'
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22 -D '$iprlookup'
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23 -E '$goterms'
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24 -F '$pathways'
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25 ]]></command>
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26 <inputs>
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27 <param type="data" name="fasta_input" label="sequences in fasta format" optional="False" format="fasta,fa"/>
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28 <param type="select" name="output_format" argument="-f" label="Output format" optional="False" multiple="True">
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29 <option value="TSV" selected="false">TSV</option>
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30 <option value="XML" selected="false">XML</option>
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31 <option value="JSON" selected="false">JSON</option>
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32 <option value="GFF3" selected="false">GFF3</option>
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33 <option value="HTML" selected="false">HTML</option>
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34 <option value="SVG" selected="false">SVG</option>
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35 </param>
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1
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36 <param type="boolean" name="disable_precalc" argument="--disable-precalc" label="disable precalc"
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37 help="Disables use of the precalculated match lookup service" optional="False" checked="True"
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38 truevalue="NO_ARGUMENT_YES" falsevalue="NO_ARGUMENT_NO"/>
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39 <param type="boolean" name="iprlookup" argument="--iprlookup" label="lookup corresponding InterPro annotation"
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40 help="Also include lookup of corresponding InterPro annotation in the TSV and GFF3 output formats"
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41 optional="False" checked="True" truevalue="NO_ARGUMENT_YES" falsevalue="NO_ARGUMENT_NO"/>
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42 <param type="boolean" name="goterms" argument="--goterms"
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43 label="switch on lookup of corresponding Gene Ontology" optional="False" checked="True"
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44 truevalue="NO_ARGUMENT_YES" falsevalue="NO_ARGUMENT_NO"/>
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45 <param type="boolean" name="pathways" argument="--pathways"
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46 label="switch on lookup of corresponding Pathway annotation" optional="False" checked="True"
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47 truevalue="NO_ARGUMENT_YES" falsevalue="NO_ARGUMENT_NO"/>
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48 </inputs>
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49 <outputs>
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3
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50 <data name="report" format="html" label="${tool.name} on ${on_string}" hidden="false"/>
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51 <data name="sink_message" format="txt" label="${tool.name} log on ${on_string}"
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52 from_work_dir="warnings_and_errors.txt" hidden="false"/>
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0
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53 </outputs>
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54 <citations>
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55 <citation type="bibtex"><![CDATA[
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56 @article{allaire2016rmarkdown,
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57 title={rmarkdown: Dynamic Documents for R, 2016},
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58 author={Allaire, J and Cheng, Joe and Xie, Yihui and McPherson, Jonathan and Chang, Winston and Allen, Jeff
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59 and Wickham, Hadley and Atkins, Aron and Hyndman, Rob},
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60 journal={R package version 0.9},
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61 volume={6},
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62 year={2016}
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63 }
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64 ]]></citation>
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65 <citation type="bibtex"><![CDATA[
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66 @book{xie2015dynamic,
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67 title={Dynamic Documents with R and knitr},
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68 author={Xie, Yihui},
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69 volume={29},
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70 year={2015},
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71 publisher={CRC Press}
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72 }
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73 ]]></citation>
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74 <citation type="bibtex"><![CDATA[@article{jones2014interproscan,
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75 title={InterProScan 5: genome-scale protein function classification},
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76 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},
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77 journal={Bioinformatics},
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78 volume={30},
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79 number={9},
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80 pages={1236--1240},
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81 year={2014},
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82 publisher={Oxford University Press}
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83 }]]></citation>
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84 </citations>
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85 </tool>
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