Mercurial > repos > iuc > bcftools_plugin_setgt
comparison bcftools_plugin_setgt.xml @ 17:a1aad8b559c6 draft
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 |
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| 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 ===================================== |