Mercurial > repos > iuc > vt_variant_tools
comparison vt_normalize.xml @ 1:16f7587ab084 draft
Uploaded
| author | iuc |
|---|---|
| date | Thu, 14 Aug 2014 09:58:02 -0400 |
| parents | 106dc0bf83c6 |
| children | e76f203fc135 |
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| 0:106dc0bf83c6 | 1:16f7587ab084 |
|---|---|
| 9 <command> | 9 <command> |
| 10 <![CDATA[ | 10 <![CDATA[ |
| 11 vt @BINARY@ | 11 vt @BINARY@ |
| 12 -o "${ outfile }" | 12 -o "${ outfile }" |
| 13 ##-q do not print options and summary [] | 13 ##-q do not print options and summary [] |
| 14 -w window size for local sorting of variants [10000] | 14 -w $window |
| 15 | 15 |
| 16 #if str( $intervals_file ) != 'None': | 16 #if str( $intervals_file ) != 'None': |
| 17 -I "${intervals_file}" | 17 -I "${intervals_file}" |
| 18 #end if | 18 #end if |
| 19 | 19 |
| 20 ##-i intervals [] | 20 ##-i intervals [] |
| 21 | 21 |
| 22 #if $reference_source.reference_source_selector != "history": | 22 #if $reference_source.reference_source_selector != "history": |
| 23 -r "${reference_source.reference_genome.fields.path}"' | 23 -r "${reference_source.reference_genome.fields.path}" |
| 24 #else: | 24 #else: |
| 25 -r "${reference_source.reference_genome}" | 25 -r "${reference_source.reference_genome}" |
| 26 #end if | 26 #end if |
| 27 | 27 |
| 28 "${ infile }" | 28 "${ infile }" |