Mercurial > repos > devteam > bwa
changeset 5:b59a6178a6e0 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit dead2eaab58698fe02b8bb068f8d859eba551e8d
| author | devteam |
|---|---|
| date | Sat, 30 Sep 2017 13:36:50 -0400 |
| parents | 774491f4a074 |
| children | a4d167793afa |
| files | bwa-mem.xml bwa_macros.xml test-data/bwa-aln-test1-fasta.bam test-data/bwa-aln-test1.bam test-data/bwa-aln-test2.bam test-data/bwa-aln-test3.bam test-data/bwa-mem-test1-fasta.bam test-data/bwa-mem-test1.bam test-data/bwa-mem-test2.bam |
| diffstat | 9 files changed, 5 insertions(+), 3 deletions(-) [+] |
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--- a/bwa-mem.xml Thu Jun 01 11:38:11 2017 -0400 +++ b/bwa-mem.xml Sat Sep 30 13:36:50 2017 -0400 @@ -1,5 +1,5 @@ <?xml version="1.0"?> -<tool id="bwa_mem" name="Map with BWA-MEM" version="@VERSION@.2"> +<tool id="bwa_mem" name="Map with BWA-MEM" version="@VERSION@.0"> <description>- map medium and long reads (> 100 bp) against reference genome</description> <macros> <import>read_group_macros.xml</import> @@ -63,6 +63,7 @@ ${analysis_type.io_options.V} ${analysis_type.io_options.Y} ${analysis_type.io_options.M} + ${analysis_type.io_options.five} #end if #end if @@ -226,6 +227,7 @@ <option value="do_not_set" selected="True">Do not set</option> </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 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 Thu Jun 01 11:38:11 2017 -0400 +++ b/bwa_macros.xml Sat Sep 30 13:36:50 2017 -0400 @@ -1,7 +1,7 @@ <macros> <import>read_group_macros.xml</import> - <token name="@VERSION@">0.7.15</token> + <token name="@VERSION@">0.7.16</token> <token name="@set_rg_string@"> #set $rg_string = "@RG\\tID:" + str($rg_id) @@ -35,7 +35,7 @@ <xml name="requirements"> <requirements> <requirement type="package" version="@VERSION@">bwa</requirement> - <requirement type="package" version="1.3.1">samtools</requirement> + <requirement type="package" version="1.5">samtools</requirement> </requirements> </xml>