<tool id="chem" name="Chemical Identifier Converter" version="master">
  <requirements>
    <container type="docker">registry.gitlab.ics.muni.cz:443/recetox/mass-spectrometry/chem_identifier_converter:master</container>
  </requirements>
  <stdio>
    <exit_code range="1:" />
    <exit_code range=":-1" />
  </stdio>
  <command><![CDATA[ cd /chem_identifier_converter && Rscript chem_identifier_converter.r
 							--inFile $input --outFile $output
  ]]>
  </command>
  <inputs>
    <param name="input" type="data" label="CSV file with input."/>
  </inputs>
  <outputs>
    <data format="csv" name="output" label="CSV file with output."/>
  </outputs>
  <help>
This is a utility for chemical identifier conversion (version 1.0.2). User can input file with different chemical identifiers (common/preffered name, IUPAC name, InChIKey, SMILES) in a CSV format (one identifier per line, no header) and will get file with all remaining identifiers. Currently, only the beforementioned 4 chemical identifiers are allowed as an input. 

Author of the Galaxy tool: Karolína Trachtová (k.trachtova@gmail.com)

If used, please cite:

Eduard Szöcs et al. (2015). webchem: zenodo release. Zenodo. 10.5281/zenodo.33823.

Kevin Horan and Thomas Girke (2018). ChemmineOB: R interface to a subset of OpenBabel functionalities. R package version 1.20.0. https://github.com/girke-lab/ChemmineOB.
  </help>
</tool>