comparison kraken2.xml @ 1:7932d09da19b draft

planemo upload for repository https://github.com/dfornika/galaxytools/blob/master/tools/kraken2 commit 593a4002db3f2513974809a94db514c05fa589f6-dirty

0:a77e88d426d9

        <requirement type="package" version="@TOOL_VERSION@">kraken2</requirement>
    </requirements>
    <version_command>kraken2 --version</version_command>
    <command detect_errors="exit_code">
        <![CDATA[
        @SET_DATABASE_PATH@ &&

        kraken2
            --threads \${GALAXY_SLOTS:-1}
            @INPUT_DATABASE@

            #if $single_paired.single_paired_selector == 'yes'
                #if $forward_input.is_of_type( 'fastq' ):
                    --fastq-input
                #else:
                    --fasta-input

            </when>
            <when value="no">
                <param format="fasta,fastq" label="Input sequences" name="input_sequences" type="data" help="FASTA or FASTQ datasets"/>
            </when>
        </conditional>
        <param name="" type="" format="" />
    </inputs>
    <outputs>
        <data name="output" format="" />
    </outputs>
    <tests>

1:7932d09da19b

        <requirement type="package" version="@TOOL_VERSION@">kraken2</requirement>
    </requirements>
    <version_command>kraken2 --version</version_command>
    <command detect_errors="exit_code">
        <![CDATA[
        kraken2
            --threads \${GALAXY_SLOTS:-1}
            @INPUT_DATABASE@
            #if $single_paired.single_paired_selector == 'yes'
                #if $forward_input.is_of_type( 'fastq' ):
                    --fastq-input
                #else:
                    --fasta-input

            </when>
            <when value="no">
                <param format="fasta,fastq" label="Input sequences" name="input_sequences" type="data" help="FASTA or FASTQ datasets"/>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data name="output" format="" />
    </outputs>
    <tests>