comparison samtools_mpileup.xml @ 5:aa0ef6f0ee89 draft

planemo upload commit 7d9b478cd03f31705266596fe4c168e719c672b6

4:c6fdfe3331d6

            #end if
        #end if
        #if str( $advanced_options.limit_by_region.limit_by_regions ) == "paste":
            -l "$pasted_regions"
        #elif str( $advanced_options.limit_by_region.limit_by_regions ) == "history"
            -l "$bed_regions"
        #end if
        #if str( $advanced_options.exclude_read_group.exclude_read_groups ) == "paste":
            -G "$excluded_read_groups"
        #elif str( $advanced_options.exclude_read_group.exclude_read_groups ) == "history"
            -G "$read_groups"
        #end if
            ${advanced_options.skip_anomalous_read_pairs}
        ${advanced_options.disable_probabilistic_realignment}
        -C "${advanced_options.coefficient_for_downgrading}"
        -d "${advanced_options.max_reads_per_bam}"
        ${advanced_options.extended_BAQ_computation}
        -q "${advanced_options.minimum_mapping_quality}"

                <param label="Coefficient for downgrading mapping quality for reads containing excessive mismatches" name="coefficient_for_downgrading" type="integer" value="0" help="--adjust-MQ; Given a read with a phred-scaled probability q of being generated from the mapped position, the new mapping quality is about sqrt((INT-q)/INT)*INT. A zero value disables this functionality; if enabled, the recommended value for BWA is 50. default=0"/>
                <param label="Max reads per BAM" max="1024" min="1" name="max_reads_per_bam" type="integer" value="250" help="--max-depth; default=250"/>
                <param checked="False" falsevalue="" label="Redo BAQ computation" name="extended_BAQ_computation" truevalue="-E" type="boolean" help="--redo-BAQ; ignore existing BQ tags"/>
                <param label="Minimum mapping quality for an alignment to be used" name="minimum_mapping_quality" type="integer" value="0" help="-min-MQ; default=0"/>
                <param label="Minimum base quality for a base to be considered" name="minimum_base_quality" type="integer" value="13" help="--min-BQ; default=13"/>
            </when>
            <when value="basic" />
        </conditional>
    </inputs>
    <outputs>

5:aa0ef6f0ee89

            #end if
        #end if
        #if str( $advanced_options.limit_by_region.limit_by_regions ) == "paste":
            -l "$pasted_regions"
        #elif str( $advanced_options.limit_by_region.limit_by_regions ) == "history"
            -l "$advanced_options.limit_by_region.bed_regions"
        #end if
        #if str( $advanced_options.exclude_read_group.exclude_read_groups ) == "paste":
            -G "$excluded_read_groups"
        #elif str( $advanced_options.exclude_read_group.exclude_read_groups ) == "history"
            -G "$advanced_options.exclude_read_group.read_groups"
        #end if
        ${advanced_options.skip_anomalous_read_pairs}
        ${advanced_options.disable_probabilistic_realignment}
        -C "${advanced_options.coefficient_for_downgrading}"
        -d "${advanced_options.max_reads_per_bam}"
        ${advanced_options.extended_BAQ_computation}
        -q "${advanced_options.minimum_mapping_quality}"

                <param label="Coefficient for downgrading mapping quality for reads containing excessive mismatches" name="coefficient_for_downgrading" type="integer" value="0" help="--adjust-MQ; Given a read with a phred-scaled probability q of being generated from the mapped position, the new mapping quality is about sqrt((INT-q)/INT)*INT. A zero value disables this functionality; if enabled, the recommended value for BWA is 50. default=0"/>
                <param label="Max reads per BAM" max="1024" min="1" name="max_reads_per_bam" type="integer" value="250" help="--max-depth; default=250"/>
                <param checked="False" falsevalue="" label="Redo BAQ computation" name="extended_BAQ_computation" truevalue="-E" type="boolean" help="--redo-BAQ; ignore existing BQ tags"/>
                <param label="Minimum mapping quality for an alignment to be used" name="minimum_mapping_quality" type="integer" value="0" help="-min-MQ; default=0"/>
                <param label="Minimum base quality for a base to be considered" name="minimum_base_quality" type="integer" value="13" help="--min-BQ; default=13"/>
                <param label="Only generate pileup in region" name="region_string" type="text" value="" help="--region; If used in conjunction with --positions, then considers the intersection of the two requests. Defaults to all sites" />
            </when>
            <when value="basic" />
        </conditional>
    </inputs>
    <outputs>