| Previous changeset 8:27250f92a01a (2022-12-03) Next changeset 10:4fd3b5d8706b (2023-03-29) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2 |
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modified:
macros.xml merge_metaphlan_tables.xml tool_data_table_conf.xml.sample tool_data_table_conf.xml.test |
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added:
test-data/test_database_versioned.loc tool-data/metaphlan_database_versioned.loc.sample |
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removed:
test-data/test_database.loc tool-data/metaphlan_database.loc.sample |
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| diff -r 27250f92a01a -r e073891b2afc macros.xml --- a/macros.xml Sat Dec 03 10:42:15 2022 +0000 +++ b/macros.xml Mon Feb 27 06:59:58 2023 +0000 |
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| @@ -1,17 +1,16 @@ <?xml version="1.0"?> <macros> - <token name="@TOOL_VERSION@">4.0.3</token> + <token name="@TOOL_VERSION@">4.0.5</token> <token name="@VERSION_SUFFIX@">0</token> - <token name="@PROFILE@">20.01</token> + <token name="@PROFILE@">22.05</token> + <!-- Metaphlan DB compatible with this version of Metaphlan + v4 introduced single genome level bins (SGB) and the index syntax differs from previous versions --> + <token name="@IDX_VERSION@">SGB</token> + <token name="@IDX_DATA_TABLE@">metaphlan_database_versioned</token> <xml name="edam_ontology"> - <edam_topics> - <edam_topic>topic_3174</edam_topic> - <edam_topic>topic_0194</edam_topic> - </edam_topics> - <edam_operations> - <edam_operation>operation_2478</edam_operation> - <edam_operation>operation_0324</edam_operation> - </edam_operations> + <xrefs> + <xref type="bio.tools">metaphlan</xref> + </xrefs> </xml> <xml name="requirements"> <requirements> |
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| diff -r 27250f92a01a -r e073891b2afc merge_metaphlan_tables.xml --- a/merge_metaphlan_tables.xml Sat Dec 03 10:42:15 2022 +0000 +++ b/merge_metaphlan_tables.xml Mon Feb 27 06:59:58 2023 +0000 |
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| @@ -5,7 +5,7 @@ </macros> <expand macro="edam_ontology"/> <expand macro="requirements"/> - <version_command>merge_metaphlan_tables.py -v</version_command> + <version_command>metaphlan -v</version_command> <command detect_errors="aggressive"><![CDATA[ merge_metaphlan_tables.py #for $element in $inputs @@ -15,20 +15,20 @@ ]]> </command> <inputs> - <param name="inputs" type="data" format="tabular,txt" multiple="true" label="Predicted taxon relative abundance tables generaed by MetaPhlAn" /> + <param name="inputs" type="data" format="tabular,txt" multiple="true" label="Predicted taxon relative abundance tables generaed by MetaPhlAn"/> </inputs> <outputs> - <data name="output" format="tabular" label="${tool.name} on ${on_string}: Merged taxon relative abundance tables" /> + <data name="output" format="tabular" label="${tool.name} on ${on_string}: Merged taxon relative abundance tables"/> </outputs> <tests> <test expect_num_outputs="1"> <param name="inputs" value="SRS014464-Anterior_nares-abundances.tabular,SRS014464-Anterior_nares-abundances.tabular"/> - <output name="output" ftype="tabular" > + <output name="output" ftype="tabular"> <assert_contents> <has_text text="k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium_accolens"/> <has_text text="dataset_"/> <has_text text="clade_name"/> - <has_line_matching expression="#.*" /> + <has_line_matching expression="#.*"/> </assert_contents> </output> </test> |
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| diff -r 27250f92a01a -r e073891b2afc test-data/test_database.loc --- a/test-data/test_database.loc Sat Dec 03 10:42:15 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,6 +0,0 @@ -# Tab separated with 4 columns: -# - value (Galaxy records this in the Galaxy DB) -# - name (Galaxy shows this in the UI) -# - value (Galaxy records this in the Galaxy DB) -# - path (folder name containing the Kraken DB) -test-db-20210409 "Test Database" test-db ${__HERE__}/test-db \ No newline at end of file |
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| diff -r 27250f92a01a -r e073891b2afc test-data/test_database_versioned.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_database_versioned.loc Mon Feb 27 06:59:58 2023 +0000 |
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| @@ -0,0 +1,7 @@ +# Tab separated with 5 columns: +# - value (Galaxy records this in the Galaxy DB) +# - name (Galaxy shows this in the UI) +# - value (Galaxy records this in the Galaxy DB) +# - path (folder name containing the Kraken DB) +# - db version (whether it is SGB of Metaphlan v4 or not) +test-db-20210409 "Test Database" test-db ${__HERE__}/test-db SGB |
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| diff -r 27250f92a01a -r e073891b2afc tool-data/metaphlan_database.loc.sample --- a/tool-data/metaphlan_database.loc.sample Sat Dec 03 10:42:15 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,4 +0,0 @@ -#This is a sample file distributed with Galaxy that enables tools -#to use a directory of metagenomics files. -#file has this format (white space characters are TAB characters) -#02_16_2014 MetaPhlAn2 clade-specific marker genes db_v20 /path/to/data \ No newline at end of file |
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| diff -r 27250f92a01a -r e073891b2afc tool-data/metaphlan_database_versioned.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/metaphlan_database_versioned.loc.sample Mon Feb 27 06:59:58 2023 +0000 |
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| @@ -0,0 +1,4 @@ +#This is a sample file distributed with Galaxy that enables tools +#to use a directory of metagenomics files. +#file has this format (white space characters are TAB characters) +#02_16_2014 MetaPhlAn2 clade-specific marker genes db_v20 /path/to/data SGB_or_legacy |
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| diff -r 27250f92a01a -r e073891b2afc tool_data_table_conf.xml.sample --- a/tool_data_table_conf.xml.sample Sat Dec 03 10:42:15 2022 +0000 +++ b/tool_data_table_conf.xml.sample Mon Feb 27 06:59:58 2023 +0000 |
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| @@ -1,6 +1,7 @@ +<?xml version="1.0"?> <tables> - <table name="metaphlan_database" comment_char="#"> - <columns>value, name, dbkey, path</columns> - <file path="tool-data/metaphlan_database.loc" /> + <table name="metaphlan_database_versioned" comment_char="#"> + <columns>value, name, dbkey, path, db_version</columns> + <file path="tool-data/metaphlan_database_versioned.loc"/> </table> </tables> |
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| diff -r 27250f92a01a -r e073891b2afc tool_data_table_conf.xml.test --- a/tool_data_table_conf.xml.test Sat Dec 03 10:42:15 2022 +0000 +++ b/tool_data_table_conf.xml.test Mon Feb 27 06:59:58 2023 +0000 |
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| @@ -1,7 +1,7 @@ <?xml version="1.0"?> <tables> - <table name="metaphlan_database" comment_char="#"> - <columns>value, name, dbkey, path</columns> - <file path="${__HERE__}/test-data/test_database.loc" /> + <table name="metaphlan_database_versioned" comment_char="#"> + <columns>value, name, dbkey, path, db_version</columns> + <file path="${__HERE__}/test-data/test_database_versioned.loc"/> </table> -</tables> \ No newline at end of file +</tables> |