Mercurial > repos > devteam > samtools_mpileup
changeset 5:aa0ef6f0ee89 draft
planemo upload commit 7d9b478cd03f31705266596fe4c168e719c672b6
| author | devteam |
|---|---|
| date | Fri, 08 May 2015 16:51:29 -0400 |
| parents | c6fdfe3331d6 |
| children | 820754ab8901 |
| files | samtools_mpileup.xml |
| diffstat | 1 files changed, 4 insertions(+), 3 deletions(-) [+] |
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--- a/samtools_mpileup.xml Tue Apr 21 16:29:10 2015 -0400 +++ b/samtools_mpileup.xml Fri May 08 16:51:29 2015 -0400 @@ -33,14 +33,14 @@ #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" + -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( $advanced_options.exclude_read_group.exclude_read_groups ) == "history" - -G "$read_groups" + -G "$advanced_options.exclude_read_group.read_groups" #end if - ${advanced_options.skip_anomalous_read_pairs} + ${advanced_options.skip_anomalous_read_pairs} ${advanced_options.disable_probabilistic_realignment} -C "${advanced_options.coefficient_for_downgrading}" -d "${advanced_options.max_reads_per_bam}" @@ -241,6 +241,7 @@ <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>