Mercurial > repos > iuc > bcftools_plugin_fixploidy

comparison bcftools_plugin_fixploidy.xml @ 5:aec8cc772e0c draft

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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">