Mercurial > repos > iuc > gtdbtk_classify_wf
changeset 2:6501b5b33988 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gtdbtk commit fab39612473d91e048868d9c122d7dd61a2bd9d4
| author | iuc |
|---|---|
| date | Tue, 25 Jul 2023 12:27:39 +0000 |
| parents | dbf1798c0dcc |
| children | f8f56dd6449f |
| files | gtdbtk_classify_wf.xml macros.xml |
| diffstat | 2 files changed, 31 insertions(+), 23 deletions(-) [+] |
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--- a/gtdbtk_classify_wf.xml Thu Feb 16 23:35:55 2023 +0000 +++ b/gtdbtk_classify_wf.xml Tue Jul 25 12:27:39 2023 +0000 @@ -9,9 +9,6 @@ mkdir input_dir && mkdir output_dir && -mkdir output_tsv_dir && -mkdir output_newick_dir && -mkdir output_fasta_dir && #for $i in $input: ## gtdbtk uses the file extension to determine the input format. #set ext = "." + $i.ext @@ -53,38 +50,38 @@ <data name="process_log" format="txt" label="${tool.name} on ${on_string} (process log)"> <filter>advanced['output_process_log'] == 'yes'</filter> </data> - <collection name="output_tsv" type="list" format="tsv" label="${tool.name} on ${on_string} (tsv)"> - <discover_datasets pattern="(?P<designation>.+)\.tsv" ext="tsv" directory="output_dir"/> + <collection name="output_align" type="list" format="fasta.gz" label="${tool.name} on ${on_string} (align)"> + <discover_datasets pattern="(?P<designation>.+)\.fasta.gz" ext="fasta.gz" directory="output_dir/align"/> + </collection> + <collection name="output_identfy" type="list" format="tsv" label="${tool.name} on ${on_string} (identify)"> + <discover_datasets pattern="(?P<designation>.+)\.tsv" ext="tsv" directory="output_dir/identify"/> </collection> - <collection name="output_newick" type="list" format="newick" label="${tool.name} on ${on_string} (newick)"> - <discover_datasets pattern="(?P<designation>.+)\.tree" ext="newick" directory="output_dir"/> + <collection name="output_classify" type="list" format="newick" label="${tool.name} on ${on_string} (classify)"> + <discover_datasets pattern="(?P<designation>.+)\.tree" ext="newick" directory="output_dir/classify"/> </collection> - <collection name="output_fasta" type="list" format="fasta" label="${tool.name} on ${on_string} (fasta)"> - <discover_datasets pattern="(?P<designation>.+)\.fasta" ext="fasta" directory="output_dir"/> + <collection name="output_summary" type="list" format="tsv" label="${tool.name} on ${on_string} (summary)"> + <discover_datasets pattern="(?P<designation>.+)\.tsv" ext="tsv" directory="output_dir"/> </collection> </outputs> <tests> <!-- The commented test here is valid if we could store the GTDB-Tk database --> <!-- - <test expect_num_outputs="3"> + <test expect_num_outputs="4"> <param name="input" value="genome_1.fna.gz" ftype="fasta.gz"/> <param name="gtdbtk_db" value="gtdbtk202"/> - <output_collection name="output_tsv" type="list" count="6"> - <element name="gtdbtk.ar122.filtered" ftype="tsv"> + <output_collection name="output_summary" type="list" count="1"> + <element name="gtdbtk.ar122.summary" ftype="tsv"> <assert_contents> - <has_size value="0"/> + <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"> <assert_contents> <has_text text="number_unique_genes"/> </assert_contents> </element> - <element name="gtdbtk.ar122.summary" ftype="tsv"> - <assert_contents> - <has_text text="genome_1_fna_gz"/> - </assert_contents> - </element> <element name="gtdbtk.bac120.markers_summary" ftype="tsv"> <assert_contents> <has_text text="genome_1_fna_gz"/> @@ -101,15 +98,25 @@ </assert_contents> </element> </output_collection> - <output_collection name="output_newick" type="list" count="1"> - <element name="gtdbtk.ar122.classify" ftype="newick"> + <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"> <assert_contents> <has_text text="GB_GCA_"/> </assert_contents> </element> </output_collection> - <output_collection name="output_fasta" type="list" count="2"> - <element name="gtdbtk.ar122.msa" ftype="fasta"> + <output_collection name="output_align" type="list" count="2"> + <element name="gtdbtk.ar122.msa" ftype="fasta.gz"> <assert_contents> <has_text text="GB_GCA_000008085"/> </assert_contents> @@ -158,3 +165,4 @@ ]]></help> <expand macro="citations"/> </tool> +
--- a/macros.xml Thu Feb 16 23:35:55 2023 +0000 +++ b/macros.xml Tue Jul 25 12:27:39 2023 +0000 @@ -1,6 +1,6 @@ <macros> <token name="@TOOL_VERSION@">2.2.2</token> - <token name="@VERSION_SUFFIX@">0</token> + <token name="@VERSION_SUFFIX@">1</token> <token name="@PROFILE@">20.09</token> <xml name="requirements"> <requirements>