comparison augur_parse.xml @ 1:892c6690a1e8 draft default tip

planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/augur commit a71ecf1b4a86227084935c6f60dfd130b7d0997b-dirty

0:20ad934c5536

          --output-metadata '$output_metadata'
    ]]></command>
    <inputs>
        <param name="sequences" type="data" format="fasta" label="Sequences"/>
        <param name="fields" type="text" label="Fields in fasta header"/>
	<param name="separator" type="text" value="|" label="Separator in fasta header"/>
    </inputs>
    <outputs>
      <data name="output_sequences" format="fasta" />
      <data name="output_metadata" format="tabular" />
    </outputs>
    <tests>
        <test>
          <param name="sequences" value="test_00_sequences.input.fasta" />
	  <param name="fields" value="strain country year" />
	  <output name="output_sequences" file="test_00_sequences.output.fasta" />
	  <output name="output_metadata" file="test_00_metadata.output.fasta" />
        </test>
    </tests>
    <help><![CDATA[
Parse delimited fields from FASTA sequence names into a TSV and FASTA file.
    ]]></help>
    <citations>
        <citation type="bibtex">
	  @article{hadfield2018nextstrain,
	    title={Nextstrain: real-time tracking of pathogen evolution},
	    author={Hadfield, James and Megill, Colin and Bell, Sidney M and Huddleston, John and Potter, Barney and Callender, Charlton and Sagulenko, Pavel and Bedford, Trevor and Neher, Richard A},
	    journal={Bioinformatics},
	    volume={34},
	    number={23},
	    pages={4121--4123},
	    year={2018},
	    publisher={Oxford University Press}
	  }
	</citation>
    </citations>
</tool>

1:892c6690a1e8

          --output-metadata '$output_metadata'
    ]]></command>
    <inputs>
        <param name="sequences" type="data" format="fasta" label="Sequences"/>
        <param name="fields" type="text" label="Fields in fasta header"/>
        <param name="separator" type="text" value="|" label="Separator in fasta header">
            <sanitizer>
                <valid initial="string.printable">
                    <remove value="&apos;"/>
                </valid>
                <mapping initial="none">
                </mapping>
            </sanitizer>
        </param>
    </inputs>
    <outputs>
        <data name="output_sequences" format="fasta" />
        <data name="output_metadata" format="tabular" />
    </outputs>
    <tests>
        <test>
            <param name="sequences" value="augur_parse_test_0_sequences.input.fasta" />
            <param name="fields" value="strain country year" />
            <output name="output_sequences" file="augur_parse_test_0_sequences.output.fasta" />
            <output name="output_metadata" file="augur_parse_test_0_metadata.output.csv" />
        </test>
    </tests>
    <help><![CDATA[
Parse delimited fields from FASTA sequence names into a TSV and FASTA file.
    ]]></help>
    <expand macro="citations" />
</tool>