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1 <tool id="ClermonTyping" name="ClermonTyping" version="1">
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2 <description>
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3 ClermonTyping: an easy-to-use and accurate in silico method for Escherichia genus strain phylotyping
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4 </description>
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5 <requirements>
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6 <requirement type="package" version="1.79">biopython</requirement>
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7 <requirement type="package" version="2.12.0">blast</requirement>
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8 <requirement type="package" version="2.17.1.1">pandoc</requirement>
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9 <requirement type="package" version="2.1.2">r-readr</requirement>
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10 <requirement type="package" version="1.0.7">r-dplyr</requirement>
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11 <requirement type="package" version="1.2.0">r-tidyr</requirement>
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12 <requirement type="package" version="1.37">r-knitr</requirement>
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13 <requirement type="package" version="1.4.0">r-stringr</requirement>
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14 <requirement type="package" version="2.11">r-markdown</requirement>
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15 </requirements>
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16 <command detect_errors="exit_code"><![CDATA[
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17 /home/galaxy/ClermonTyping/clermonTyping.sh --fasta ${input} --name Analyse
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18 ]]></command>
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19 <inputs>
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20 <param name="input" format="fasta" type="data" label="Select contigs file in fasta format." help="Fasta format containing contigs."/>
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21 </inputs>
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22 <outputs>
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23 <data name="html" format="html" label="html output file" from_work_dir="Analyse/Analyse.html"/>
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24 <data name="phylogroup" format="tsv" label="Phylogroup found" from_work_dir="Analyse/Analyse_phylogroups.txt"/>
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25 </outputs>
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26 <help>
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27 Script usage :
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28 -h : print this message and exit
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29 -v : print the version and exit
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30 --fasta : fasta contigs file(s). If multiple files, they must be separated by an arobase (@) value
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31 --name : name for this analysis (optional)
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32 --threshold : option for ClermontTyping, do not use contigs under this size (optional)
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33 --minimal : output a minimal set of files (optional)
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34 --fastafile : file with path of fasta contig file. One file by line (optional)
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35 --summary : file with path of *_phylogroups.txt. One file by line (optional)
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36 </help>
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37 </tool>
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