comparison kraken2.xml @ 8:d120504e741a draft

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

7:7b9218c5e126

        <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}
	    --db '$kraken2_database'
            #if $single_paired.single_paired_selector == 'yes'
                '${single_paired.forward_input}' '${single_paired.reverse_input}'

                <param format="fasta,fastq" name="input_pair" type="data_collection" collection_type="paired" label="Collection of paired reads" help="FASTA or FASTQ datasets" />
            </when>
            <when value="yes">
                <param format="fasta,fastq" name="forward_input" type="data" label="Forward strand" help="FASTA or FASTQ dataset"/>
                <param format="fasta,fastq" name="reverse_input" type="data" label="Reverse strand" help="FASTA or FASTQ dataset"/>
                <param name="check_names" type="boolean" checked="False" truevalue="--paired --check-names" falsevalue="--paired" label="Verify read names match" help="--check-names" />
            </when>
            <when value="no">
                <param format="fasta,fastq" label="Input sequences" name="input_sequences" type="data" help="FASTA or FASTQ datasets"/>
            </when>
        </conditional>

8:d120504e741a

        <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}
	    --db '$kraken2_database'
            #if $single_paired.single_paired_selector == 'yes'
                '${single_paired.forward_input}' '${single_paired.reverse_input}'

                <param format="fasta,fastq" name="input_pair" type="data_collection" collection_type="paired" label="Collection of paired reads" help="FASTA or FASTQ datasets" />
            </when>
            <when value="yes">
                <param format="fasta,fastq" name="forward_input" type="data" label="Forward strand" help="FASTA or FASTQ dataset"/>
                <param format="fasta,fastq" name="reverse_input" type="data" label="Reverse strand" help="FASTA or FASTQ dataset"/>
            </when>
            <when value="no">
                <param format="fasta,fastq" label="Input sequences" name="input_sequences" type="data" help="FASTA or FASTQ datasets"/>
            </when>
        </conditional>