Mercurial > repos > iuc > metaphlan
changeset 6:2131d7dca455 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2
| author | iuc |
|---|---|
| date | Mon, 27 Feb 2023 07:01:00 +0000 |
| parents | 6dee4abadccb |
| children | ec368db926f4 |
| files | macros.xml metaphlan.xml test-data/test_database.loc test-data/test_database_versioned.loc tool-data/metaphlan_database.loc.sample tool-data/metaphlan_database_versioned.loc.sample tool_data_table_conf.xml.sample tool_data_table_conf.xml.test |
| diffstat | 8 files changed, 101 insertions(+), 98 deletions(-) [+] |
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--- a/macros.xml Sat Dec 03 10:43:21 2022 +0000 +++ b/macros.xml Mon Feb 27 07:01:00 2023 +0000 @@ -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>
--- a/metaphlan.xml Sat Dec 03 10:43:21 2022 +0000 +++ b/metaphlan.xml Mon Feb 27 07:01:00 2023 +0000 @@ -263,15 +263,16 @@ <option value="history">From history</option> </param> <when value="cached"> - <param name="cached_db" label="Cached database with clade-specific marker genes" type="select"> - <options from_data_table="metaphlan_database"> - <validator message="No MetaPhlAn database is available" type="no_options" /> + <param name="cached_db" type="select" label="Cached database with clade-specific marker genes"> + <options from_data_table="@IDX_DATA_TABLE@"> + <filter type="static_value" column="4" value="@IDX_VERSION@"/> + <validator message="No compatible MetaPhlAn database is available" type="no_options"/> </options> </param> </when> <when value="history"> <param argument="--bowtie2db" type="data" format="fasta" label="Database with clade-specific marker genes from history"/> - <param argument="--mpa_pkl" type="data" format="json" label="Metadata associate to the database with clade-specific marker genes from history"/> + <param argument="--mpa_pkl" type="data" format="json" label="Metadata associated to the database with clade-specific marker genes from history"/> </when> </conditional> </section> @@ -435,6 +436,7 @@ </assert_contents> </output> <output_collection name="levels" type="list" > + <element name="all" ftype="tabular"> <assert_contents> <has_text text="class"/> @@ -442,21 +444,6 @@ <has_n_lines n="1"/> </assert_contents> </element> - <element name="kingdom" ftype="tabular"> - <assert_contents> - <has_text text="kingdom_id"/> - <has_n_columns n="3"/> - <has_n_lines n="1"/> - </assert_contents> - </element> - <element name="phylum" ftype="tabular"> - <assert_contents> - <has_text text="phylum_id"/> - <not_has_text text="kingdom_id"/> - <has_n_columns n="3"/> - <has_n_lines n="1"/> - </assert_contents> - </element> <element name="class" ftype="tabular"> <assert_contents> <has_text text="class_id"/> @@ -465,14 +452,6 @@ <has_n_lines n="1"/> </assert_contents> </element> - <element name="order" ftype="tabular"> - <assert_contents> - <has_text text="order_id"/> - <not_has_text text="class_id"/> - <has_n_columns n="3"/> - <has_n_lines n="1"/> - </assert_contents> - </element> <element name="family" ftype="tabular"> <assert_contents> <has_text text="family_id"/> @@ -489,6 +468,29 @@ <has_n_lines n="1"/> </assert_contents> </element> + <element name="kingdom" ftype="tabular"> + <assert_contents> + <has_text text="kingdom_id"/> + <has_n_columns n="3"/> + <has_n_lines n="1"/> + </assert_contents> + </element> + <element name="order" ftype="tabular"> + <assert_contents> + <has_text text="order_id"/> + <not_has_text text="class_id"/> + <has_n_columns n="3"/> + <has_n_lines n="1"/> + </assert_contents> + </element> + <element name="phylum" ftype="tabular"> + <assert_contents> + <has_text text="phylum_id"/> + <not_has_text text="kingdom_id"/> + <has_n_columns n="3"/> + <has_n_lines n="1"/> + </assert_contents> + </element> <element name="species" ftype="tabular"> <assert_contents> <has_text text="species_id"/> @@ -588,21 +590,6 @@ <has_n_columns n="17"/> </assert_contents> </element> - <element name="kingdom" ftype="tabular"> - <assert_contents> - <has_text text="kingdom_id"/> - <has_text text="Bacteria"/> - <has_n_columns n="3"/> - </assert_contents> - </element> - <element name="phylum" ftype="tabular"> - <assert_contents> - <has_text text="phylum_id"/> - <not_has_text text="kingdom_id"/> - <has_text text="Firmicutes"/> - <has_n_columns n="3"/> - </assert_contents> - </element> <element name="class" ftype="tabular"> <assert_contents> <has_text text="class_id"/> @@ -611,14 +598,6 @@ <has_n_columns n="3"/> </assert_contents> </element> - <element name="order" ftype="tabular"> - <assert_contents> - <has_text text="order_id"/> - <not_has_text text="class_id"/> - <has_text text="Propionibacteriales"/> - <has_n_columns n="3"/> - </assert_contents> - </element> <element name="family" ftype="tabular"> <assert_contents> <has_text text="family_id"/> @@ -635,6 +614,29 @@ <has_n_columns n="3"/> </assert_contents> </element> + <element name="kingdom" ftype="tabular"> + <assert_contents> + <has_text text="kingdom_id"/> + <has_text text="Bacteria"/> + <has_n_columns n="3"/> + </assert_contents> + </element> + <element name="order" ftype="tabular"> + <assert_contents> + <has_text text="order_id"/> + <not_has_text text="class_id"/> + <has_text text="Propionibacteriales"/> + <has_n_columns n="3"/> + </assert_contents> + </element> + <element name="phylum" ftype="tabular"> + <assert_contents> + <has_text text="phylum_id"/> + <not_has_text text="kingdom_id"/> + <has_text text="Firmicutes"/> + <has_n_columns n="3"/> + </assert_contents> + </element> <element name="species" ftype="tabular"> <assert_contents> <has_text text="species_id"/> @@ -988,20 +990,6 @@ <has_n_columns n="9"/> </assert_contents> </element> - <element name="kingdom" ftype="tabular"> - <assert_contents> - <has_text text="kingdom"/> - <has_text text="Bacteria"/> - <has_n_columns n="2"/> - </assert_contents> - </element> - <element name="phylum" ftype="tabular"> - <assert_contents> - <has_text text="phylum"/> - <has_text text="Firmicutes"/> - <has_n_columns n="2"/> - </assert_contents> - </element> <element name="class" ftype="tabular"> <assert_contents> <has_text text="class"/> @@ -1009,13 +997,6 @@ <has_n_columns n="2"/> </assert_contents> </element> - <element name="order" ftype="tabular"> - <assert_contents> - <has_text text="order"/> - <has_text text="Propionibacteriales"/> - <has_n_columns n="2"/> - </assert_contents> - </element> <element name="family" ftype="tabular"> <assert_contents> <has_text text="family"/> @@ -1030,6 +1011,27 @@ <has_n_columns n="2"/> </assert_contents> </element> + <element name="kingdom" ftype="tabular"> + <assert_contents> + <has_text text="kingdom"/> + <has_text text="Bacteria"/> + <has_n_columns n="2"/> + </assert_contents> + </element> + <element name="order" ftype="tabular"> + <assert_contents> + <has_text text="order"/> + <has_text text="Propionibacteriales"/> + <has_n_columns n="2"/> + </assert_contents> + </element> + <element name="phylum" ftype="tabular"> + <assert_contents> + <has_text text="phylum"/> + <has_text text="Firmicutes"/> + <has_n_columns n="2"/> + </assert_contents> + </element> <element name="species" ftype="tabular"> <assert_contents> <has_text text="species"/>
--- a/test-data/test_database.loc Sat Dec 03 10:43:21 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -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
--- /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 @@ -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 ${__HERE__}/test-db SGB
--- a/tool-data/metaphlan_database.loc.sample Sat Dec 03 10:43:21 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -#This is a sample file distributed with Galaxy that enables tools -#to use a directory of metagenomics files. -#file has this format (white space characters are TAB characters) -#02_16_2014 MetaPhlAn2 clade-specific marker genes db_v20 /path/to/data \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/metaphlan_database_versioned.loc.sample Mon Feb 27 07:01:00 2023 +0000 @@ -0,0 +1,4 @@ +#This is a sample file distributed with Galaxy that enables tools +#to use a directory of metagenomics files. +#file has this format (white space characters are TAB characters) +#02_16_2014 MetaPhlAn2 clade-specific marker genes db_v20 /path/to/data SGB_or_legacy
--- a/tool_data_table_conf.xml.sample Sat Dec 03 10:43:21 2022 +0000 +++ b/tool_data_table_conf.xml.sample Mon Feb 27 07:01:00 2023 +0000 @@ -1,6 +1,7 @@ +<?xml version="1.0"?> <tables> - <table name="metaphlan_database" comment_char="#"> - <columns>value, name, dbkey, path</columns> - <file path="tool-data/metaphlan_database.loc" /> + <table name="metaphlan_database_versioned" comment_char="#"> + <columns>value, name, dbkey, path, db_version</columns> + <file path="tool-data/metaphlan_database_versioned.loc"/> </table> </tables>
--- a/tool_data_table_conf.xml.test Sat Dec 03 10:43:21 2022 +0000 +++ b/tool_data_table_conf.xml.test Mon Feb 27 07:01:00 2023 +0000 @@ -1,7 +1,7 @@ <?xml version="1.0"?> <tables> - <table name="metaphlan_database" comment_char="#"> - <columns>value, name, dbkey, path</columns> - <file path="${__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>