comparison kraken2.xml @ 3:4a9da2b6c2e3 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken2/kraken2/ commit fed92935f1f0b52173d2fddbdd2bbf44e802b51e"

2:328c607150ff

        kraken2
            --threads \${GALAXY_SLOTS:-1}
            --db '${kraken2_database.fields.path}'

            #if $quick:
                --quick
            #end if

            #if $single_paired.single_paired_selector == "yes"
                --paired 
                '${single_paired.forward_input}' '${single_paired.reverse_input}'
            #elif $single_paired.single_paired_selector == "collection":

                #end if
            #end if

            --confidence '${confidence}'
            --minimum-base-quality '${min_base_quality}'

            #if $use_names:
                --use-names
            #end if

            #if $report.create_report:
                --report '${report_output}'
                #if $report.use_mpa_style:
                    --use-mpa-style
                #end if
                #if $report.report_zero_counts:
                    --report-zero-counts
                #end if
            #end if

            > '${output}'
    ]]></command>
    <inputs>

            </when>
            <when value="no">
                <param format="@INTYPES@" label="Input sequences" name="input_sequences" type="data"/>
            </when>
        </conditional>
        <param name="use_names" type="boolean" label="Print scientific names instead of just taxids"/>
        <param name="confidence"  type="float" label="Confidence" value="0.0" help="Confidence score threshold. Must be in [0, 1]">
            <validator type="in_range" min="0.0" max="1.0" message="Confidence score threshold should be between 0 and 1" />
        </param>
        <param name="min_base_quality" type="integer" label="Minimum Base Quality" value="0" help="Minimum base quality used in classification (only effective with FASTQ input)"/>
        <param name="quick" type="boolean" label="Enable quick operation" help="Quick operation (use first hit)"/>
        <param name="split_reads" type="boolean" label="Split classified and unclassified outputs?" help="Sets --unclassified-out and --classified-out"/>

        <section name="report" title="Create Report" expanded="false">
            <param name="create_report" type="boolean"  label="Print a report with aggregrate counts/clade to file" help="--report" optional="true"/>
            <param name="use_mpa_style" type="boolean" label="Format report output like Kraken 1's kraken-mpa-report" help="--use-mpa-style" optional="true"/>
            <param name="report_zero_counts" type="boolean" label="Report counts for ALL taxa, even if counts are zero" help="--report-zero-counts" optional="true"/>
        </section>

        <expand macro="input_database"/>  
    </inputs>
    <outputs>

3:4a9da2b6c2e3

        kraken2
            --threads \${GALAXY_SLOTS:-1}
            --db '${kraken2_database.fields.path}'

            $quick

            #if $single_paired.single_paired_selector == "yes"
                --paired 
                '${single_paired.forward_input}' '${single_paired.reverse_input}'
            #elif $single_paired.single_paired_selector == "collection":

                #end if
            #end if

            --confidence '${confidence}'
            --minimum-base-quality '${min_base_quality}'
            --minimum-hit-groups '${minimum_hit_groups}'

            $use_names

            #if $report.create_report:
                --report '${report_output}'
                $report.use_mpa_style
                $report.report_zero_counts:
                $report.report_minimizer_data:
            #end if

            > '${output}'
    ]]></command>
    <inputs>

            </when>
            <when value="no">
                <param format="@INTYPES@" label="Input sequences" name="input_sequences" type="data"/>
            </when>
        </conditional>
        <param argument="--use-names" type="boolean" truevalue="--use-names" falsevalue="" label="Print scientific names instead of just taxids"/>
        <param argument="--confidence" type="float" label="Confidence" value="0.0" min="0" max="1" help="Confidence score threshold. Must be in [0, 1]"/>
        <param argument="--minimum-base-quality" name="min_base_quality" type="integer" label="Minimum Base Quality" value="0" help="Minimum base quality used in classification (only effective with FASTQ input)"/>
        <param argument="--minimum-hit-groups" type="integer" label="Minimum hit goups" value="2" help="Number of overlapping k-mers sharing the same minimizer needed to make a call" />
        <param argument="--quick" type="boolean" truevalue="--quick" falsevalue="" label="Enable quick operation" help="Quick operation (use first hit)"/>
        <param name="split_reads" type="boolean" label="Split classified and unclassified outputs?" help="Sets --unclassified-out and --classified-out"/>

        <section name="report" title="Create Report" expanded="false">
            <param name="create_report" type="boolean"  label="Print a report with aggregrate counts/clade to file" help="--report" />
            <param argument="--use-mpa-style" type="boolean" truevalue="--use-mpa-style" falsevalue="" label="Format report output like Kraken 1's kraken-mpa-report" />
            <param argument="--report-zero-counts" type="boolean" truevalue="--report-zero-counts" falsevalue="" label="Report counts for ALL taxa, even if counts are zero" />
            <param argument="--report-minimizer-data" type="boolean" truevalue="--report-minimizer-data" falsevalue="" label="Report minimizer data" help="Report minimizer and distinct minimizer count information in addition to normal Kraken report" />
        </section>

        <expand macro="input_database"/>  
    </inputs>
    <outputs>