Mercurial > repos > iuc > bcftools_plugin_fixploidy
comparison bcftools_plugin_fixploidy.xml @ 5:aec8cc772e0c draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
| author | iuc |
|---|---|
| date | Thu, 13 Apr 2017 17:45:30 -0400 |
| parents | b7dc6f8084ce |
| children | 12152af85697 |
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| 4:b7dc6f8084ce | 5:aec8cc772e0c |
|---|---|
| 11 <command detect_errors="aggressive"><![CDATA[ | 11 <command detect_errors="aggressive"><![CDATA[ |
| 12 @PREPARE_ENV@ | 12 @PREPARE_ENV@ |
| 13 @PREPARE_INPUT_FILE@ | 13 @PREPARE_INPUT_FILE@ |
| 14 #set $section = $sec_restrict | 14 #set $section = $sec_restrict |
| 15 @PREPARE_TARGETS_FILE@ | 15 @PREPARE_TARGETS_FILE@ |
| 16 @PREPARE_REGIONS_FILE@ | |
| 16 | 17 |
| 17 bcftools plugin @EXECUTABLE@ | 18 bcftools plugin @EXECUTABLE@ |
| 18 | 19 |
| 19 ## VCF input section | 20 ## VCF input section |
| 20 #set $section = $sec_restrict | 21 #set $section = $sec_restrict |
| 36 #if $section.sex: | 37 #if $section.sex: |
| 37 --sex "${section.sex}" | 38 --sex "${section.sex}" |
| 38 #end if | 39 #end if |
| 39 ## Only default tag GT is currently accepted | 40 ## Only default tag GT is currently accepted |
| 40 --tags "$section.tags" | 41 --tags "$section.tags" |
| 41 > "$output_file" | 42 > '$output_file' |
| 42 ]]> | 43 ]]> |
| 43 </command> | 44 </command> |
| 44 <inputs> | 45 <inputs> |
| 45 <expand macro="macro_input" /> | 46 <expand macro="macro_input" /> |
| 46 <section name="sec_restrict" expanded="false" title="Restrict to"> | 47 <section name="sec_restrict" expanded="false" title="Restrict to"> |