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

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

<tool id="augur_parse" name="augur parse" version="@TOOL_VERSION@+galaxy0">
    <description></description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">augur</requirement>
    </requirements>
    <version_command>augur --version</version_command>
    <command detect_errors="exit_code"><![CDATA[
        augur parse
          --sequences '$sequences'
          --fields $fields
          --separator '$separator'
          --output-sequences '$output_sequences'
          --output-metadata '$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>