Mercurial > repos > iuc > data_manager_build_coreprofiler
changeset 4:a1e8960e1629 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_coreprofiler commit adc61f2c22d06e320a8a3776d5255f14ddd94e78
| author | iuc |
|---|---|
| date | Thu, 08 Jan 2026 10:29:36 +0000 |
| parents | 8caa09336d6f |
| children | |
| files | data_manager/data_manager_build_coreprofiler_download.xml data_manager_conf.xml test-data/coreprofiler_scheme.loc.test test-data/coreprofiler_versioned_scheme.loc.test tool-data/coreprofiler_scheme.loc.sample tool-data/coreprofiler_versioned_scheme.loc.sample tool_data_table_conf.xml.sample tool_data_table_conf.xml.test |
| diffstat | 8 files changed, 31 insertions(+), 31 deletions(-) [+] |
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--- a/data_manager/data_manager_build_coreprofiler_download.xml Thu Dec 18 15:21:21 2025 +0000 +++ b/data_manager/data_manager_build_coreprofiler_download.xml Thu Jan 08 10:29:36 2026 +0000 @@ -2,7 +2,7 @@ <description></description> <macros> <token name="@TOOL_VERSION@">2.0.0</token> - <token name="@VERSION_SUFFIX@">1</token> + <token name="@VERSION_SUFFIX@">2</token> <token name="@PROFILE@">22.05</token> <xml name="version_command"> <version_command><![CDATA[$ coreprofiler --version]]></version_command> @@ -120,7 +120,7 @@ { "data_tables":{ - "coreprofiler_scheme":[ + "coreprofiler_versioned_scheme":[ { "value": "coreprofiler_downloaded_${today}-${scheme_name}-${scheme_desc}-${scheme_loci}-${scheme_db}-${db_version}", "name": "${scheme_name}: ${scheme_desc} [${scheme_loci} loci] (${scheme_db} - ${db_date_version})", @@ -278,7 +278,7 @@ </conditional> <output name="out_file"> <assert_contents> - <has_text text='"coreprofiler_scheme":'/> + <has_text text='"coreprofiler_versioned_scheme":'/> <has_text_matching expression='"value": "coreprofiler_downloaded_[0-9-]{10}-borrelia_3-cgMLST-639-pubmlst-no_token"'/> <has_text text='"name": "borrelia_3: cgMLST [639 loci] (pubmlst - version before 2025)"'/> <has_text_matching expression='"tool_version": "[0-9.]+"'/> @@ -298,7 +298,7 @@ </conditional> <output name="out_file"> <assert_contents> - <has_text text='"coreprofiler_scheme":'/> + <has_text text='"coreprofiler_versioned_scheme":'/> <has_text_matching expression='"value": "coreprofiler_downloaded_[0-9-]{10}-yersinia_1-Yersinia_cgMLST-500-bigsdb-no_token"'/> <has_text text='"name": "yersinia_1: Yersinia_cgMLST [500 loci] (bigsdb - version before 2025)"'/> <has_text_matching expression='"tool_version": "[0-9.]+"'/> @@ -317,7 +317,7 @@ </conditional> <output name="out_file"> <assert_contents> - <has_text text='"coreprofiler_scheme":'/> + <has_text text='"coreprofiler_versioned_scheme":'/> <has_text_matching expression='"value": "coreprofiler_downloaded_[0-9-]{10}-escherichia_v1-cgMLST-2513-enterobase-no_token"'/> <has_text_matching expression='"name": "escherichia_v1: cgMLST \[2513 loci\] \(enterobase - downloaded on [0-9-]{10}\)"'/> <has_text_matching expression='"tool_version": "[0-9.]+"'/> @@ -336,7 +336,7 @@ </conditional> <output name="out_file"> <assert_contents> - <has_text text='"coreprofiler_scheme":'/> + <has_text text='"coreprofiler_versioned_scheme":'/> <has_text_matching expression='"value": "coreprofiler_downloaded_[0-9-]{10}-mgallisepticum-Mycoplasma_gallisepticum-425-cgmlstorg-no_token"'/> <has_text_matching expression='"name": "mgallisepticum: Mycoplasma_gallisepticum \[425 loci\] \(cgmlstorg - downloaded on [0-9-]{10}\)"'/> <has_text_matching expression='"tool_version": "[0-9.]+"'/>
--- a/data_manager_conf.xml Thu Dec 18 15:21:21 2025 +0000 +++ b/data_manager_conf.xml Thu Jan 08 10:29:36 2026 +0000 @@ -1,7 +1,7 @@ <?xml version="1.0"?> <data_managers> <data_manager tool_file="data_manager/data_manager_build_coreprofiler_download.xml" id="data_manager_build_coreprofiler_download"> - <data_table name="coreprofiler_scheme"> <!-- Defines a Data Table to be modified. --> + <data_table name="coreprofiler_versioned_scheme"> <!-- Defines a Data Table to be modified. --> <output> <!-- Handle the output of the Data Manager Tool --> <column name="value"/> <!-- columns that are going to be specified by the Data Manager Tool --> <column name="name"/> <!-- columns that are going to be specified by the Data Manager Tool -->
--- a/test-data/coreprofiler_scheme.loc.test Thu Dec 18 15:21:21 2025 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,10 +0,0 @@ -#This is a tab separated file describing the location of CoreProfiler scheme -#used for the CoreProfiler tool -# -#file has this format (white space characters are TAB characters) -# -#The columns are: -#value name tool_version database path db_path scheme_path -# -#For example -#coreprofiler_downloaded_20250625_klebsiella_3_scgMLST634_632_loci_bigsdb klebsiella_3: scgMLST634 [632 loci] (BIGSdb) 1.1.1 bigsdb coreprofiler_klebsiella_3 db_klebsiella_3/klebsiella_3.fasta scheme_klebsiella_3
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/coreprofiler_versioned_scheme.loc.test Thu Jan 08 10:29:36 2026 +0000 @@ -0,0 +1,10 @@ +#This is a tab separated file describing the location of CoreProfiler scheme +#used for the CoreProfiler tool +# +#file has this format (white space characters are TAB characters) +# +#The columns are: +#value name tool_version database path db_path scheme_path +# +#For example +#coreprofiler_downloaded_20250625_klebsiella_3_scgMLST634_632_loci_bigsdb klebsiella_3: scgMLST634 [632 loci] (BIGSdb) 1.1.1 bigsdb coreprofiler_klebsiella_3 db_klebsiella_3/klebsiella_3.fasta scheme_klebsiella_3
--- a/tool-data/coreprofiler_scheme.loc.sample Thu Dec 18 15:21:21 2025 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,10 +0,0 @@ -#This is a tab separated file describing the location of CoreProfiler scheme -#used for the CoreProfiler tool -# -#file has this format (white space characters are TAB characters) -# -#The columns are: -#value name tool_version database path db_path scheme_path -# -#For example -#coreprofiler_downloaded_20250625_klebsiella_3_scgMLST634_632_loci_bigsdb klebsiella_3: scgMLST634 [632 loci] (BIGSdb) 1.1.1 bigsdb coreprofiler_klebsiella_3 db_klebsiella_3/klebsiella_3.fasta scheme_klebsiella_3 \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/coreprofiler_versioned_scheme.loc.sample Thu Jan 08 10:29:36 2026 +0000 @@ -0,0 +1,10 @@ +#This is a tab separated file describing the location of CoreProfiler scheme +#used for the CoreProfiler tool +# +#file has this format (white space characters are TAB characters) +# +#The columns are: +#value name tool_version database path db_path scheme_path +# +#For example +#coreprofiler_downloaded_20250625_klebsiella_3_scgMLST634_632_loci_bigsdb klebsiella_3: scgMLST634 [632 loci] (BIGSdb) 1.1.1 bigsdb coreprofiler_klebsiella_3 db_klebsiella_3/klebsiella_3.fasta scheme_klebsiella_3 \ No newline at end of file
--- a/tool_data_table_conf.xml.sample Thu Dec 18 15:21:21 2025 +0000 +++ b/tool_data_table_conf.xml.sample Thu Jan 08 10:29:36 2026 +0000 @@ -1,6 +1,6 @@ <tables> - <table name="coreprofiler_scheme" comment_char="#"> + <table name="coreprofiler_versioned_scheme" comment_char="#"> <columns>value, name, tool_version, database, path, db_path, scheme_path</columns> - <file path="tool-data/coreprofiler_scheme.loc"/> + <file path="tool-data/coreprofiler_versioned_scheme.loc"/> </table> </tables> \ No newline at end of file
--- a/tool_data_table_conf.xml.test Thu Dec 18 15:21:21 2025 +0000 +++ b/tool_data_table_conf.xml.test Thu Jan 08 10:29:36 2026 +0000 @@ -1,6 +1,6 @@ <tables> - <table name="coreprofiler_scheme" comment_char="#"> + <table name="coreprofiler_versioned_scheme" comment_char="#"> <columns>value, name, tool_version, database, path, db_path, scheme_path</columns> - <file path="${__HERE__}/test-data/coreprofiler_scheme.loc.test"/> + <file path="${__HERE__}/test-data/coreprofiler_versioned_scheme.loc.test"/> </table> </tables> \ No newline at end of file