Mercurial > repos > p.lucas > clermontyping
comparison ClermonTyping_wrapper.xml @ 0:e93c20bad6b0 draft
First upload wrapper
| author | p.lucas |
|---|---|
| date | Mon, 14 Feb 2022 11:15:04 +0000 |
| parents | |
| children | cec55ef9cce5 |
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| -1:000000000000 | 0:e93c20bad6b0 |
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| 1 <tool id="ClermonTyping" name="ClermonTyping" version="1"> | |
| 2 <description> | |
| 3 ClermonTyping: an easy-to-use and accurate in silico method for Escherichia genus strain phylotyping | |
| 4 </description> | |
| 5 <requirements> | |
| 6 <requirement type="package" version="1.79">biopython</requirement> | |
| 7 <requirement type="package" version="2.12.0">blast</requirement> | |
| 8 <requirement type="package" version="2.17.1.1">pandoc</requirement> | |
| 9 <requirement type="package" version="2.1.2">r-readr</requirement> | |
| 10 <requirement type="package" version="1.0.7">r-dplyr</requirement> | |
| 11 <requirement type="package" version="1.2.0">r-tidyr</requirement> | |
| 12 <requirement type="package" version="1.37">r-knitr</requirement> | |
| 13 <requirement type="package" version="1.4.0">r-stringr</requirement> | |
| 14 <requirement type="package" version="2.11">r-markdown</requirement> | |
| 15 </requirements> | |
| 16 <command detect_errors="exit_code"><![CDATA[ | |
| 17 /home/galaxy/ClermonTyping/clermonTyping.sh --fasta ${input} --name Analyse | |
| 18 ]]></command> | |
| 19 <inputs> | |
| 20 <param name="input" format="fasta" type="data" label="Select contigs file in fasta format." help="Fasta format containing contigs."/> | |
| 21 </inputs> | |
| 22 <outputs> | |
| 23 <data name="html" format="html" label="html output file" from_work_dir="Analyse/Analyse.html"/> | |
| 24 <data name="phylogroup" format="tsv" label="Phylogroup found" from_work_dir="Analyse/Analyse_phylogroups.txt"/> | |
| 25 </outputs> | |
| 26 <help> | |
| 27 Script usage : | |
| 28 -h : print this message and exit | |
| 29 -v : print the version and exit | |
| 30 --fasta : fasta contigs file(s). If multiple files, they must be separated by an arobase (@) value | |
| 31 --name : name for this analysis (optional) | |
| 32 --threshold : option for ClermontTyping, do not use contigs under this size (optional) | |
| 33 --minimal : output a minimal set of files (optional) | |
| 34 --fastafile : file with path of fasta contig file. One file by line (optional) | |
| 35 --summary : file with path of *_phylogroups.txt. One file by line (optional) | |
| 36 </help> | |
| 37 </tool> |