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Fix bug in setting Bowtie2 parameters.

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This commit is contained in:
Jeremy Goecks
2012-06-08 13:48:37 -04:00
parent ab9afd1af2
commit a08c0c03ce
1 changed files with 6 additions and 4 deletions
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tools/sr_mapping/bowtie2_wrapper.xml
+6 -4
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@@ -35,10 +35,12 @@
## Set params.
--settings=$params.settingsType
#if str($params.align_type) == "end_to_end":
--end-to-end --preset-alignment=$params.preset.align_preset_select
#else:
--local --preset-alignment=$params.preset.align_preset_select-local
#if $params.settingsType == "full":
#if str($params.align_type) == "end_to_end":
--end-to-end --preset-alignment=$params.preset.align_preset_select
#else:
--local --preset-alignment=$params.preset.align_preset_select-local
#end if
#end if
</command>
<inputs>