| Previous changeset 5:6dee4abadccb (2022-12-03) Next changeset 7:ec368db926f4 (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 metaphlan.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 6dee4abadccb -r 2131d7dca455 macros.xml --- a/macros.xml Sat Dec 03 10:43:21 2022 +0000 +++ b/macros.xml Mon Feb 27 07:01:00 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 6dee4abadccb -r 2131d7dca455 metaphlan.xml --- a/metaphlan.xml Sat Dec 03 10:43:21 2022 +0000 +++ b/metaphlan.xml Mon Feb 27 07:01:00 2023 +0000 |
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| b'@@ -263,15 +263,16 @@\n <option value="history">From history</option>\n </param>\n <when value="cached">\n- <param name="cached_db" label="Cached database with clade-specific marker genes" type="select">\n- <options from_data_table="metaphlan_database">\n- <validator message="No MetaPhlAn database is available" type="no_options" />\n+ <param name="cached_db" type="select" label="Cached database with clade-specific marker genes">\n+ <options from_data_table="@IDX_DATA_TABLE@">\n+ <filter type="static_value" column="4" value="@IDX_VERSION@"/>\n+ <validator message="No compatible MetaPhlAn database is available" type="no_options"/>\n </options>\n </param>\n </when>\n <when value="history">\n <param argument="--bowtie2db" type="data" format="fasta" label="Database with clade-specific marker genes from history"/>\n- <param argument="--mpa_pkl" type="data" format="json" label="Metadata associate to the database with clade-specific marker genes from history"/>\n+ <param argument="--mpa_pkl" type="data" format="json" label="Metadata associated to the database with clade-specific marker genes from history"/>\n </when>\n </conditional>\n </section>\n@@ -435,6 +436,7 @@\n </assert_contents>\n </output>\n <output_collection name="levels" type="list" >\n+ \n <element name="all" ftype="tabular">\n <assert_contents>\n <has_text text="class"/>\n@@ -442,21 +444,6 @@\n <has_n_lines n="1"/>\n </assert_contents>\n </element>\n- <element name="kingdom" ftype="tabular">\n- <assert_contents>\n- <has_text text="kingdom_id"/>\n- <has_n_columns n="3"/>\n- <has_n_lines n="1"/>\n- </assert_contents>\n- </element>\n- <element name="phylum" ftype="tabular">\n- <assert_contents>\n- <has_text text="phylum_id"/>\n- <not_has_text text="kingdom_id"/>\n- <has_n_columns n="3"/>\n- <has_n_lines n="1"/>\n- </assert_contents>\n- </element>\n <element name="class" ftype="tabular">\n <assert_contents>\n <has_text text="class_id"/>\n@@ -465,14 +452,6 @@\n <has_n_lines n="1"/>\n </assert_contents>\n </element>\n- <element name="order" ftype="tabular">\n- <assert_contents>\n- <has_text text="order_id"/>\n- <not_has_text text="class_id"/>\n- <has_n_columns n="3"/>\n- <has_n_lines n="1"/>\n- </assert_contents>\n- </element>\n <element name="family" ftype="tabular">\n <assert_contents>\n <has_text text="family_id"/>\n@@ -489,6 +468,29 @@\n <has_n_lines n="1"/>\n </assert_contents>\n </element>\n+ <element name="kingdom" ftype="tabular">\n+ <assert_contents>\n+ <has_text text="kingdom_id"/>\n+ <has_n_columns n="3"/>\n+ <has_n_lines n="1"/>\n+ </assert_contents>\n+ </element>\n+ <element name="order" ftype="tabular">\n+ <assert_contents>\n+ '..b' <element name="kingdom" ftype="tabular">\n+ <assert_contents>\n+ <has_text text="kingdom_id"/>\n+ <has_text text="Bacteria"/>\n+ <has_n_columns n="3"/>\n+ </assert_contents>\n+ </element>\n+ <element name="order" ftype="tabular">\n+ <assert_contents>\n+ <has_text text="order_id"/>\n+ <not_has_text text="class_id"/>\n+ <has_text text="Propionibacteriales"/>\n+ <has_n_columns n="3"/>\n+ </assert_contents>\n+ </element>\n+ <element name="phylum" ftype="tabular">\n+ <assert_contents>\n+ <has_text text="phylum_id"/>\n+ <not_has_text text="kingdom_id"/>\n+ <has_text text="Firmicutes"/>\n+ <has_n_columns n="3"/>\n+ </assert_contents>\n+ </element>\n <element name="species" ftype="tabular">\n <assert_contents>\n <has_text text="species_id"/>\n@@ -988,20 +990,6 @@\n <has_n_columns n="9"/>\n </assert_contents>\n </element>\n- <element name="kingdom" ftype="tabular">\n- <assert_contents>\n- <has_text text="kingdom"/>\n- <has_text text="Bacteria"/>\n- <has_n_columns n="2"/>\n- </assert_contents>\n- </element>\n- <element name="phylum" ftype="tabular">\n- <assert_contents>\n- <has_text text="phylum"/>\n- <has_text text="Firmicutes"/>\n- <has_n_columns n="2"/>\n- </assert_contents>\n- </element>\n <element name="class" ftype="tabular">\n <assert_contents>\n <has_text text="class"/>\n@@ -1009,13 +997,6 @@\n <has_n_columns n="2"/>\n </assert_contents>\n </element>\n- <element name="order" ftype="tabular">\n- <assert_contents>\n- <has_text text="order"/>\n- <has_text text="Propionibacteriales"/>\n- <has_n_columns n="2"/>\n- </assert_contents>\n- </element>\n <element name="family" ftype="tabular">\n <assert_contents>\n <has_text text="family"/>\n@@ -1030,6 +1011,27 @@\n <has_n_columns n="2"/>\n </assert_contents>\n </element>\n+ <element name="kingdom" ftype="tabular">\n+ <assert_contents>\n+ <has_text text="kingdom"/>\n+ <has_text text="Bacteria"/>\n+ <has_n_columns n="2"/>\n+ </assert_contents>\n+ </element>\n+ <element name="order" ftype="tabular">\n+ <assert_contents>\n+ <has_text text="order"/>\n+ <has_text text="Propionibacteriales"/>\n+ <has_n_columns n="2"/>\n+ </assert_contents>\n+ </element>\n+ <element name="phylum" ftype="tabular">\n+ <assert_contents>\n+ <has_text text="phylum"/>\n+ <has_text text="Firmicutes"/>\n+ <has_n_columns n="2"/>\n+ </assert_contents>\n+ </element>\n <element name="species" ftype="tabular">\n <assert_contents>\n <has_text text="species"/>\n' |
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| diff -r 6dee4abadccb -r 2131d7dca455 test-data/test_database.loc --- a/test-data/test_database.loc Sat Dec 03 10:43:21 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 6dee4abadccb -r 2131d7dca455 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 07:01:00 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 6dee4abadccb -r 2131d7dca455 tool-data/metaphlan_database.loc.sample --- a/tool-data/metaphlan_database.loc.sample Sat Dec 03 10:43:21 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 6dee4abadccb -r 2131d7dca455 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 07:01:00 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 6dee4abadccb -r 2131d7dca455 tool_data_table_conf.xml.sample --- a/tool_data_table_conf.xml.sample Sat Dec 03 10:43:21 2022 +0000 +++ b/tool_data_table_conf.xml.sample Mon Feb 27 07:01:00 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 6dee4abadccb -r 2131d7dca455 tool_data_table_conf.xml.test --- a/tool_data_table_conf.xml.test Sat Dec 03 10:43:21 2022 +0000 +++ b/tool_data_table_conf.xml.test Mon Feb 27 07:01:00 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> |