| Previous changeset 6:3cb37af59360 (2020-09-05) Next changeset 8:96cac424c870 (2022-01-25) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7" |
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modified:
eggnog_macros.xml eggnog_mapper.xml tool_data_table_conf.xml.sample tool_data_table_conf.xml.test |
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added:
test-data/cached_locally/eggnog_mapper_db_versioned.loc tool-data/eggnog_mapper_db_versioned.loc.sample |
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removed:
test-data/cached_locally/eggnog_mapper_db.loc tool-data/eggnog_mapper_db.loc.sample |
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| diff -r 3cb37af59360 -r 4e4c6329f6cd eggnog_macros.xml --- a/eggnog_macros.xml Sat Sep 05 07:21:28 2020 +0000 +++ b/eggnog_macros.xml Fri Feb 19 18:54:25 2021 +0000 |
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| @@ -1,7 +1,14 @@ <?xml version="1.0"?> <macros> <token name="@VERSION@">2.0.1</token> - <token name="@EGGNOG_DB_VERSION@">5.0</token> + <token name="@EGGNOG_DB_VERSION@">2.0</token> + <!-- + # Versionning is super confusing: + # eggnog-mapper 1.* needed a db v4.5 (based on eggnog v4.5) + # eggnog-mapper 2.0 needs a db v2.0 (based on eggnog v5.0) + # db v4.5 are not compatible with eggnog-mapper 2.0 + --> + <token name="@IDX_VERSION@">2.0</token> <xml name="citations"> <citations> <citation type="doi">10.1093/nar/gkv1248</citation> @@ -47,7 +54,7 @@ <yield /> <output name="out_file"> <assert_contents> - <has_text text="eggnog_mapper_db" /> + <has_text text="eggnog_mapper_db_versioned" /> <has_text text="@EGGNOG_DB_VERSION@" /> </assert_contents> </output> |
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| diff -r 3cb37af59360 -r 4e4c6329f6cd eggnog_mapper.xml --- a/eggnog_mapper.xml Sat Sep 05 07:21:28 2020 +0000 +++ b/eggnog_mapper.xml Fri Feb 19 18:54:25 2021 +0000 |
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| @@ -1,4 +1,4 @@ -<tool id="eggnog_mapper" name="eggNOG Mapper" version="@VERSION@"> +<tool id="eggnog_mapper" name="eggNOG Mapper" version="@VERSION@+galaxy1"> <description>functional sequence annotation by orthology</description> <macros> <import>eggnog_macros.xml</import> @@ -42,7 +42,9 @@ <inputs> <param name="input" type="data" format="fasta" label="Fasta sequences to annotate"/> <param name="eggnog_data" type="select" label="Version of eggNOG Database"> - <options from_data_table="eggnog_mapper_db"/> + <options from_data_table="eggnog_mapper_db_versioned"> + <filter type="static_value" column="3" value="@IDX_VERSION@" /> + </options> </param> <param name="translate" type="boolean" truevalue="--translate" falsevalue="" checked="false" label="Are these coding DNA sequences that need to be translated?"/> @@ -243,15 +245,15 @@ <param name="eggnog_data" value="@EGGNOG_DB_VERSION@"/> <param name="no_annot" value="true"/> <param name="no_file_comments" value="true"/> - <output name="seed_orthologs" file="DIA_nlim.emapper.seed_orthologs" ftype="tabular"/> + <output name="seed_orthologs" file="DIA_nlim.emapper.seed_orthologs" ftype="tabular" compare="sim_size"/> </test> <test> <param name="input" value="Nmar_0135.fa" ftype="fasta"/> <param name="eggnog_data" value="@EGGNOG_DB_VERSION@"/> <!-- not passed in test, but required for test to work --> <param name="report_orthologs" value="true"/> <param name="no_file_comments" value="true"/> - <output name="seed_orthologs" file="DIA_nlim.emapper.seed_orthologs" ftype="tabular"/> - <output name="annotations" file="DIA_nlim.emapper.annotations" ftype="tabular"/> + <output name="seed_orthologs" file="DIA_nlim.emapper.seed_orthologs" ftype="tabular" compare="sim_size"/> + <output name="annotations" file="DIA_nlim.emapper.annotations" ftype="tabular" compare="sim_size"/> <output name="annotations_orthologs" file="DIA_nlim.emapper.annotations_orthologs" ftype="tabular"/> </test> <test> @@ -262,8 +264,8 @@ <section name="annotation_options"> <param name="tax_scope" value="651137" /> </section> - <output name="seed_orthologs" file="scoped.emapper.seed_orthologs" ftype="tabular"/> - <output name="annotations" file="scoped.emapper.annotations" ftype="tabular"/> + <output name="seed_orthologs" file="scoped.emapper.seed_orthologs" ftype="tabular" compare="sim_size"/> + <output name="annotations" file="scoped.emapper.annotations" ftype="tabular" compare="sim_size"/> <output name="annotations_orthologs" file="scoped.emapper.annotations_orthologs" ftype="tabular"/> </test> </tests> |
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| diff -r 3cb37af59360 -r 4e4c6329f6cd test-data/cached_locally/eggnog_mapper_db.loc --- a/test-data/cached_locally/eggnog_mapper_db.loc Sat Sep 05 07:21:28 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,2 +0,0 @@ -#value name path -5.0 eggNOG_5.0 ${__HERE__} |
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| diff -r 3cb37af59360 -r 4e4c6329f6cd test-data/cached_locally/eggnog_mapper_db_versioned.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cached_locally/eggnog_mapper_db_versioned.loc Fri Feb 19 18:54:25 2021 +0000 |
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| @@ -0,0 +1,2 @@ +#value name path version +2.0 eggNOG_2.0 ${__HERE__} 2.0 |
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| diff -r 3cb37af59360 -r 4e4c6329f6cd tool-data/eggnog_mapper_db.loc.sample --- a/tool-data/eggnog_mapper_db.loc.sample Sat Sep 05 07:21:28 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,22 +0,0 @@ -#This is a sample file distributed with Galaxy that enables tools -#to use a directory of eggnog_mapper data files. -# -# eggnog-mapper requires the following files to be installed in the data directory: -# https://github.com/jhcepas/eggnog-mapper/blob/master/data/og2level.tsv.gz -# http://eggnog5.embl.de/download/emapperdb-5.0.0/eggnog.db.gz -# A complete diamond database is available from: -# http://eggnog5.embl.de/download/emapperdb-5.0.0/eggnog_proteins.dmnd.gz -# -# The python script download_eggnog_data.py, -# included with eggnog_mapper, can be used to download the files to the correct directory -# -# The near-equivalence of columns "value" and "db" is needed for the tests to work, -# and for the setting of --data_dir to the parent directory of eggnog.db -# The complicated eggNOG database structure makes passing custom HMM databases somewhat tricky. -# See test-data/cached_locally/eggnog_mapper.loc for how this was done with the included test databases -# In all other cases, when the appropriate HMM database (for example, "thaNOG") was downloaded from eggnogdb.embl.de, -# value and db should be the same (in the example, both should be "thaNOG") -# -# -#db_version name path -#5.0 eggnog_5.0 /path/to/directory/that/contains/eggnog.db |
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| diff -r 3cb37af59360 -r 4e4c6329f6cd tool-data/eggnog_mapper_db_versioned.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/eggnog_mapper_db_versioned.loc.sample Fri Feb 19 18:54:25 2021 +0000 |
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| @@ -0,0 +1,22 @@ +#This is a sample file distributed with Galaxy that enables tools +#to use a directory of eggnog_mapper data files. +# +# eggnog-mapper requires the following files to be installed in the data directory: +# https://github.com/jhcepas/eggnog-mapper/blob/master/data/og2level.tsv.gz +# http://eggnog5.embl.de/download/emapperdb-5.0.0/eggnog.db.gz +# A complete diamond database is available from: +# http://eggnog5.embl.de/download/emapperdb-5.0.0/eggnog_proteins.dmnd.gz +# +# The python script download_eggnog_data.py, +# included with eggnog_mapper, can be used to download the files to the correct directory +# +# The near-equivalence of columns "value" and "db" is needed for the tests to work, +# and for the setting of --data_dir to the parent directory of eggnog.db +# The complicated eggNOG database structure makes passing custom HMM databases somewhat tricky. +# See test-data/cached_locally/eggnog_mapper.loc for how this was done with the included test databases +# In all other cases, when the appropriate HMM database (for example, "thaNOG") was downloaded from eggnogdb.embl.de, +# value and db should be the same (in the example, both should be "thaNOG") +# +# +#db_version name path +#5.0 eggnog_5.0 /path/to/directory/that/contains/eggnog.db |
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| diff -r 3cb37af59360 -r 4e4c6329f6cd tool_data_table_conf.xml.sample --- a/tool_data_table_conf.xml.sample Sat Sep 05 07:21:28 2020 +0000 +++ b/tool_data_table_conf.xml.sample Fri Feb 19 18:54:25 2021 +0000 |
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| @@ -1,7 +1,7 @@ <tables> <!-- Locations of all eggnog_mapper data --> - <table name="eggnog_mapper_db" comment_char="#" allow_duplicate_entries="False"> - <columns>value,name,path</columns> - <file path="tool-data/eggnog_mapper_db.loc" /> + <table name="eggnog_mapper_db_versioned" comment_char="#" allow_duplicate_entries="False"> + <columns>value,name,path,version</columns> + <file path="tool-data/eggnog_mapper_db_versioned.loc" /> </table> </tables> |
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| diff -r 3cb37af59360 -r 4e4c6329f6cd tool_data_table_conf.xml.test --- a/tool_data_table_conf.xml.test Sat Sep 05 07:21:28 2020 +0000 +++ b/tool_data_table_conf.xml.test Fri Feb 19 18:54:25 2021 +0000 |
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| @@ -1,7 +1,7 @@ <tables> <!-- Locations of all eggnog_mapper data --> - <table name="eggnog_mapper_db" comment_char="#"> - <columns>value,name,path</columns> - <file path="${__HERE__}/test-data/cached_locally/eggnog_mapper_db.loc" /> + <table name="eggnog_mapper_db_versioned" comment_char="#" allow_duplicate_entries="False"> + <columns>value,name,path,version</columns> + <file path="${__HERE__}/test-data/cached_locally/eggnog_mapper_db_versioned.loc" /> </table> </tables> |