Mercurial > repos > iuc > bcftools_plugin_setgt

comparison bcftools_plugin_setgt.xml @ 17:a1aad8b559c6 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 087a38fc2eade9f3a286d672ba61571b0b69a797
author iuc
date Mon, 26 Sep 2022 18:07:19 +0000
parents 40daf124be88
children a730269af659
comparison
equal deleted inserted replaced
16:40daf124be88 17:a1aad8b559c6
17 @PREPARE_REGIONS_FILE@ 17 @PREPARE_REGIONS_FILE@
18 bcftools plugin @EXECUTABLE@ 18 bcftools plugin @EXECUTABLE@
19 19
20 ## VCF input section 20 ## VCF input section
21 #set $section = $sec_restrict 21 #set $section = $sec_restrict
22 @INCLUDE@
23 @EXCLUDE@
24 @REGIONS@ 22 @REGIONS@
25 @TARGETS@ 23 @TARGETS@
26 24
27 @OUTPUT_TYPE@ 25 @OUTPUT_TYPE@
28 @THREADS@ 26 @THREADS@
33 ## Plugin section 31 ## Plugin section
34 #set $section = $sec_plugin 32 #set $section = $sec_plugin
35 -- 33 --
36 --target-gt '$section.target_gt' 34 --target-gt '$section.target_gt'
37 --new-gt '$section.new_gt' 35 --new-gt '$section.new_gt'
36
37 #set $section = $sec_restrict
38 @INCLUDE@
39 @EXCLUDE@
38 > '$output_file' 40 > '$output_file'
39 ]]> 41 ]]>
40 </command> 42 </command>
41 <inputs> 43 <inputs>
42 <expand macro="macro_input" /> 44 <expand macro="macro_input" />
80 <assert_contents> 82 <assert_contents>
81 <has_text text="0/0:245" /> 83 <has_text text="0/0:245" />
82 </assert_contents> 84 </assert_contents>
83 </output> 85 </output>
84 </test> 86 </test>
87 <test>
88 <param name="input_file" ftype="vcf" value="plugin1.vcf" />
89 <section name="sec_restrict">
90 <param name="exclude" value="FMT/GQ>20"/>
91 </section>
92 <section name="sec_plugin">
93 <param name="target_gt" value="q" />
94 <param name="new_gt" value="." />
95 </section>
96 <param name="output_type" value="v" />
97 <output name="output_file">
98 <assert_contents>
99 <has_text text="DP4=1,2,3,4;INDEL;STR=test" />
100 <has_n_lines n="38"/>
101 </assert_contents>
102 </output>
103 </test>
85 </tests> 104 </tests>
86 <help><![CDATA[ 105 <help><![CDATA[
87 ===================================== 106 =====================================
88 bcftools @EXECUTABLE@ plugin 107 bcftools @EXECUTABLE@ plugin
89 ===================================== 108 =====================================