Mercurial > repos > devteam > bwa
changeset 16:be4e38d127ae draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit e1191c87a0fccfafa0f23c3bd09f416a6700b387
| author | devteam |
|---|---|
| date | Tue, 21 Nov 2017 09:11:39 -0500 |
| parents | 4d82cf59895e |
| children | d1228ec6233f |
| files | bwa-mem.xml bwa_macros.xml |
| diffstat | 2 files changed, 3 insertions(+), 1 deletions(-) [+] |
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--- a/bwa-mem.xml Sat Sep 30 13:37:06 2017 -0400 +++ b/bwa-mem.xml Tue Nov 21 09:11:39 2017 -0500 @@ -64,6 +64,7 @@ ${analysis_type.io_options.Y} ${analysis_type.io_options.M} ${analysis_type.io_options.five} + ${analysis_type.io_options.q} #end if #end if @@ -228,6 +229,7 @@ </param> <when value="set"> <param name="five" argument="-5" type="boolean" truevalue="-5" falsevalue="" label="For split alignment, take alignment with smallest coordinate as primary" help="Useful for HiC data"/> + <param argument="-q" type="boolean" truevalue="-q" falsevalue="" label="Don't lower MAPQ for split alignment" help="By default the MAPQ score of a supplementary alignment will be lowered to the primary alignment score."/> <param name="T" type="integer" value="30" label="Minimum score to output" help="-T; default=30"/> <param name="h" type="integer" value="5" label="If there are less than THIS VALUE hits with score >80% of the max score, output them all in the XA tag" help="-h; default=5" /> <param name="a" type="boolean" truevalue="-a" falsevalue="" label="Output all alignments for single-ends or unpaired paired-ends" help="-a; These alignments will be flagged as secondary alignments"/>
--- a/bwa_macros.xml Sat Sep 30 13:37:06 2017 -0400 +++ b/bwa_macros.xml Tue Nov 21 09:11:39 2017 -0500 @@ -1,7 +1,7 @@ <macros> <import>read_group_macros.xml</import> - <token name="@VERSION@">0.7.16</token> + <token name="@VERSION@">0.7.17</token> <token name="@set_rg_string@"> #set $rg_string = "@RG\\tID:" + str($rg_id)