Mercurial > repos > iuc > extract_metaphlan_database
changeset 6:5eccd3d336a3 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2
| author | iuc |
|---|---|
| date | Mon, 27 Feb 2023 07:00:39 +0000 |
| parents | b4c750fe0fe3 |
| children | 2e38deed28ee |
| files | extract_metaphlan_database.xml macros.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, 33 insertions(+), 31 deletions(-) [+] |
line wrap: on
line diff
--- a/extract_metaphlan_database.xml Sat Dec 03 10:42:36 2022 +0000 +++ b/extract_metaphlan_database.xml Mon Feb 27 07:00:39 2023 +0000 @@ -20,14 +20,15 @@ ]]></command> <inputs> <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" /> + <options from_data_table="@IDX_DATA_TABLE@"> + <filter type="static_value" column="4" value="@IDX_VERSION@"/> + <validator message="No MetaPhlAn database is available" type="no_options"/> </options> </param> </inputs> <outputs> - <data name="sequences" format="fasta" label="${tool.name} on ${on_string}: Marker seqeunces from MetaPhlAn database" /> - <data name="metadata" format="json" label="${tool.name} on ${on_string}: Marker metadata from MetaPhlAn database" /> + <data name="sequences" format="fasta" label="${tool.name} on ${on_string}: Marker seqeunces from MetaPhlAn database"/> + <data name="metadata" format="json" label="${tool.name} on ${on_string}: Marker metadata from MetaPhlAn database"/> </outputs> <tests> <test expect_num_outputs="2">
--- a/macros.xml Sat Dec 03 10:42:36 2022 +0000 +++ b/macros.xml Mon Feb 27 07:00:39 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/test-data/test_database.loc Sat Dec 03 10:42:36 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 07:00:39 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 ${__HERE__}/test-db SGB
--- a/tool-data/metaphlan_database.loc.sample Sat Dec 03 10:42:36 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -#This is a sample file distributed with Galaxy that enables tools -#to use a directory of metagenomics files. -#file has this format (white space characters are TAB characters) -#02_16_2014 MetaPhlAn2 clade-specific marker genes db_v20 /path/to/data \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/metaphlan_database_versioned.loc.sample Mon Feb 27 07:00:39 2023 +0000 @@ -0,0 +1,4 @@ +#This is a sample file distributed with Galaxy that enables tools +#to use a directory of metagenomics files. +#file has this format (white space characters are TAB characters) +#02_16_2014 MetaPhlAn2 clade-specific marker genes db_v20 /path/to/data SGB_or_legacy
--- a/tool_data_table_conf.xml.sample Sat Dec 03 10:42:36 2022 +0000 +++ b/tool_data_table_conf.xml.sample Mon Feb 27 07:00:39 2023 +0000 @@ -1,6 +1,7 @@ +<?xml version="1.0"?> <tables> - <table name="metaphlan_database" comment_char="#"> - <columns>value, name, dbkey, path</columns> - <file path="tool-data/metaphlan_database.loc" /> + <table name="metaphlan_database_versioned" comment_char="#"> + <columns>value, name, dbkey, path, db_version</columns> + <file path="tool-data/metaphlan_database_versioned.loc"/> </table> </tables>
--- a/tool_data_table_conf.xml.test Sat Dec 03 10:42:36 2022 +0000 +++ b/tool_data_table_conf.xml.test Mon Feb 27 07:00:39 2023 +0000 @@ -1,7 +1,7 @@ <?xml version="1.0"?> <tables> - <table name="metaphlan_database" comment_char="#"> - <columns>value, name, dbkey, path</columns> - <file path="${__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>