Mercurial > repos > dfornika > data_manager_build_kraken2_database
changeset 62:38c99b294264 draft
"planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_kraken2_database/ commit 6f21145d4103d33c227f52dc55a7d3dcf52f4f5d-dirty"
| author | dfornika |
|---|---|
| date | Wed, 23 Oct 2019 14:18:06 -0400 |
| parents | bf6408089cbc |
| children | 80e778af6c6c |
| files | data_manager/kraken2_build_database.py data_manager/kraken2_build_database.xml data_manager_conf.xml |
| diffstat | 3 files changed, 4 insertions(+), 5 deletions(-) [+] |
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--- a/data_manager/kraken2_build_database.py Mon Jul 29 15:53:28 2019 -0400 +++ b/data_manager/kraken2_build_database.py Wed Oct 23 14:18:06 2019 -0400 @@ -89,7 +89,7 @@ '--clean', '--db', database_path ] - + subprocess.check_call(['kraken2-build'] + args, cwd=target_directory) data_table_entry = {
--- a/data_manager/kraken2_build_database.xml Mon Jul 29 15:53:28 2019 -0400 +++ b/data_manager/kraken2_build_database.xml Wed Oct 23 14:18:06 2019 -0400 @@ -1,11 +1,11 @@ <?xml version="1.0"?> -<tool id="kraken2_build_database" name="Kraken2" tool_type="manage_data" version="2.0.8_beta"> +<tool id="kraken2_build_database" name="Kraken2" tool_type="manage_data" version="2.0.8_beta_galaxy1"> <macros> <xml name="common_params"> <param name="kmer_len" type="integer" value="35" label="K-mer length in BP" /> <param name="minimizer_len" type="integer" value="31" label="Minimizer length" /> <param name="minimizer_spaces" type="integer" value="6" label="Minimizer spaces" /> - <param name="clean" type="boolean" truevalue="--clean" falsevalue="" label="Clean up extra files" /> + <param name="clean" type="boolean" truevalue="--clean" falsevalue="" checked="true" label="Clean up extra files" /> </xml> </macros> <description>database builder</description> @@ -87,7 +87,6 @@ <param name="custom_fasta" value="adapter.fa" /> <param name="custom_database_name" value="database" /> <param name="skip_maps" value="true" /> - <param name="clean" value="true" /> <output name="out_file" value="kraken2_custom_data_manager.json" /> </test> </tests>
--- a/data_manager_conf.xml Mon Jul 29 15:53:28 2019 -0400 +++ b/data_manager_conf.xml Wed Oct 23 14:18:06 2019 -0400 @@ -1,5 +1,5 @@ <data_managers> - <data_manager tool_file="data_manager/kraken2_build_database.xml" id="kraken2_build_database" version="2.0.8_beta"> + <data_manager tool_file="data_manager/kraken2_build_database.xml" id="kraken2_build_database" version="2.0.8_beta_galaxy1"> <data_table name="kraken2_databases"> <output> <column name="value"/>