Mercurial > repos > iuc > gtdbtk_classify_wf
changeset 4:65d52c693b8e draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gtdbtk commit 94a1996b09d7597793f823307cbac6208e20f1d1
| author | iuc |
|---|---|
| date | Fri, 01 Mar 2024 07:19:45 +0000 |
| parents | f8f56dd6449f |
| children | a68b985913ab |
| files | gtdbtk_classify_wf.xml macros.xml test-data/gtdbtk_database.loc |
| diffstat | 3 files changed, 11 insertions(+), 21 deletions(-) [+] |
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--- a/gtdbtk_classify_wf.xml Fri Feb 09 21:40:53 2024 +0000 +++ b/gtdbtk_classify_wf.xml Fri Mar 01 07:19:45 2024 +0000 @@ -71,16 +71,16 @@ <!-- <test expect_num_outputs="4"> <param name="input" value="genome_1.fna.gz" ftype="fasta.gz"/> - <param name="gtdbtk_db" value="gtdbtk202"/> + <param name="gtdbtk_db" value="gtdbtk214"/> <output_collection name="output_summary" type="list" count="1"> - <element name="gtdbtk.ar122.summary" ftype="tsv"> + <element name="gtdbtk.ar53.summary" ftype="tsv"> <assert_contents> <has_text text="user_genome"/> </assert_contents> </element> </output_collection> <output_collection name="output_identfy" type="list" count="4"> - <element name="gtdbtk.ar122.markers_summary" ftype="tsv"> + <element name="gtdbtk.ar53.markers_summary" ftype="tsv"> <assert_contents> <has_text text="number_unique_genes"/> </assert_contents> @@ -101,30 +101,20 @@ </assert_contents> </element> </output_collection> - <output_collection name="output_classify" type="list" count="3"> - <element name="gtdbtk.ar122.classify.tree.6" ftype="newick"> - <assert_contents> - <has_text text="GB_GCA_"/> - </assert_contents> - </element> - <element name="gtdbtk.ar122" ftype="newick"> - <assert_contents> - <has_text text="user_genome"/> - </assert_contents> - </element> - <element name="gtdbtk.backbone.ar122.classify" ftype="newick"> + <output_collection name="output_classify" type="list" count="1"> + <element name="gtdbtk.ar53.classify" ftype="newick"> <assert_contents> <has_text text="GB_GCA_"/> </assert_contents> </element> </output_collection> <output_collection name="output_align" type="list" count="2"> - <element name="gtdbtk.ar122.msa" ftype="fasta.gz"> + <element name="gtdbtk.ar53.msa" ftype="fasta.gz" decompress="true"> <assert_contents> <has_text text="GB_GCA_000008085"/> </assert_contents> </element> - <element name="gtdbtk.ar122.user_msa" ftype="fasta"> + <element name="gtdbtk.ar53.user_msa" ftype="fasta.gz" decompress="true"> <assert_contents> <has_text text="genome_1_fna_gz"/> </assert_contents>
--- a/macros.xml Fri Feb 09 21:40:53 2024 +0000 +++ b/macros.xml Fri Mar 01 07:19:45 2024 +0000 @@ -1,7 +1,7 @@ <macros> - <token name="@TOOL_VERSION@">2.2.2</token> - <token name="@VERSION_SUFFIX@">1</token> - <token name="@PROFILE@">20.09</token> + <token name="@TOOL_VERSION@">2.3.2</token> + <token name="@VERSION_SUFFIX@">0</token> + <token name="@PROFILE@">22.05</token> <xml name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@">gtdbtk</requirement>
--- a/test-data/gtdbtk_database.loc Fri Feb 09 21:40:53 2024 +0000 +++ b/test-data/gtdbtk_database.loc Fri Mar 01 07:19:45 2024 +0000 @@ -23,4 +23,4 @@ #drwxr-sr-x 4 gvk G-824019 4096 Apr 21 2021 pplacer/ #drwxr-sr-x 2 gvk G-824019 4096 Apr 20 2021 radii/ #drwxr-sr-x 2 gvk G-824019 4096 Apr 20 2021 taxonomy/ -gtdbtk202 GTDB-Tk database v202 ${__HERE__}/gtdbtk202 +gtdbtk214 GTDB-Tk database v214 ${__HERE__}/gtdbtk214/