Mercurial > repos > iuc > bcftools_plugin_setgt
changeset 19:9891ba926fbe draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 087a38fc2eade9f3a286d672ba61571b0b69a797
| author | iuc |
|---|---|
| date | Mon, 26 Sep 2022 17:25:22 +0000 |
| parents | 7f0c5f32d68b |
| children | f092a4bd543e |
| files | bcftools_plugin_setgt.xml macros.xml |
| diffstat | 2 files changed, 22 insertions(+), 3 deletions(-) [+] |
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--- a/bcftools_plugin_setgt.xml Tue Sep 20 12:26:24 2022 +0000 +++ b/bcftools_plugin_setgt.xml Mon Sep 26 17:25:22 2022 +0000 @@ -19,8 +19,6 @@ ## VCF input section #set $section = $sec_restrict -@INCLUDE@ -@EXCLUDE@ @REGIONS@ @TARGETS@ @@ -35,6 +33,10 @@ -- --target-gt '$section.target_gt' --new-gt '$section.new_gt' + +#set $section = $sec_restrict +@INCLUDE@ +@EXCLUDE@ > '$output_file' ]]> </command> @@ -82,6 +84,23 @@ </assert_contents> </output> </test> + <test> + <param name="input_file" ftype="vcf" value="plugin1.vcf" /> + <section name="sec_restrict"> + <param name="exclude" value="FMT/GQ>20"/> + </section> + <section name="sec_plugin"> + <param name="target_gt" value="q" /> + <param name="new_gt" value="." /> + </section> + <param name="output_type" value="v" /> + <output name="output_file"> + <assert_contents> + <has_text text="DP4=1,2,3,4;INDEL;STR=test" /> + <has_n_lines n="38"/> + </assert_contents> + </output> + </test> </tests> <help><![CDATA[ =====================================
--- a/macros.xml Tue Sep 20 12:26:24 2022 +0000 +++ b/macros.xml Mon Sep 26 17:25:22 2022 +0000 @@ -1,6 +1,6 @@ <macros> <token name="@TOOL_VERSION@">1.15.1</token> - <token name="@VERSION_SUFFIX@">0</token> + <token name="@VERSION_SUFFIX@">1</token> <token name="@PROFILE@">20.01</token> <xml name="bio_tools"> <xrefs>