| Previous changeset 0:b1805f086b66 (2019-02-27) Next changeset 2:18523fd8bec9 (2019-02-27) |
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Commit message:
planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_kraken2_database/ commit 9b4d704c147761201fa9f1450fcf5ba6871104d8-dirty |
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modified:
data_manager/kraken2_standard_database_builder.xml data_manager_conf.xml |
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added:
data_manager/kraken2_custom_database_builder.xml |
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removed:
data_manager/kraken2_database_builder.xml |
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| diff -r b1805f086b66 -r f9a7275b1cad data_manager/kraken2_custom_database_builder.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager/kraken2_custom_database_builder.xml Wed Feb 27 20:48:06 2019 -0500 |
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| @@ -0,0 +1,50 @@ +<?xml version="1.0"?> +<tool id="kraken2_custom_database_builder" name="Kraken2 Custom Database Builder" tool_type="manage_data" version="2.0.7_beta"> + <description>database builder</description> + <requirements> + <requirement type="package" version="2.0.7_beta">kraken2</requirement> + </requirements> + <version_command>kraken2 -version | head -n 1 | awk '{print $NF}'</version_command> + <command detect_errors="exit_code"> + <![CDATA[ + #set $library_list = str($libraries).split(',') + mkdir kraken2-database && cd kraken2-database && + kraken2-build --threads \${GALAXY_SLOTS:-1} --download-taxonomy --db '${database_name}' && + #for $library in $library_list: + #if str($library) != 'None': + kraken2-build --threads \${GALAXY_SLOTS:-1} --download-library $library --db '${database_name}' && + #end if + #end for + #for $fasta in $input_fasta: + #if str($fasta) != 'None': + kraken2-build --threads \${GALAXY_SLOTS:-1} --db '${database_name}' --add-to-library '$fasta' && + #end if + #end for + kraken2-build --threads \${GALAXY_SLOTS:-1} --db '${database_name}' --build --kmer-len ${kmer_len} --minimizer-len ${minimizer_len} && + cd .. && + python '$__tool_directory__/make_json.py' --db '${database_name}' --out '${out_file}' + ]]> + </command> + <inputs> + <param name="database_name" type="text" label="Name for this database" /> + <param name="libraries" type="select" multiple="true" label="Select partial library to download"> + <option value="archaea">Archaea</option> + <option value="bacteria">Bacteria</option> + <option value="plasmid">Plasmid</option> + <option value="viral">Viral</option> + <option value="human">Human</option> + </param> + <param name="input_fasta" type="data" format="fasta" multiple="True" optional="true" label="Select history item" /> + <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" /> + </inputs> + <outputs> + <data name="out_file" format="data_manager_json" /> + </outputs> + <help> + </help> + <citations> + <citation type="doi">10.1186/gb-2014-15-3-r46</citation> + </citations> +</tool> |
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| diff -r b1805f086b66 -r f9a7275b1cad data_manager/kraken2_database_builder.xml --- a/data_manager/kraken2_database_builder.xml Wed Feb 27 20:42:33 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,50 +0,0 @@ -<?xml version="1.0"?> -<tool id="kraken2_database_builder" name="Kraken" tool_type="manage_data" version="2.0.7_beta"> - <description>database builder</description> - <requirements> - <requirement type="package" version="2.0.7_beta">kraken2</requirement> - </requirements> - <version_command>kraken2 -version | head -n 1 | awk '{print $NF}'</version_command> - <command detect_errors="exit_code"> - <![CDATA[ - #set $library_list = str($libraries).split(',') - mkdir kraken2-database && cd kraken2-database && - kraken2-build --threads \${GALAXY_SLOTS:-1} --download-taxonomy --db '${database_name}' && - #for $library in $library_list: - #if str($library) != 'None': - kraken2-build --threads \${GALAXY_SLOTS:-1} --download-library $library --db '${database_name}' && - #end if - #end for - #for $fasta in $input_fasta: - #if str($fasta) != 'None': - kraken2-build --threads \${GALAXY_SLOTS:-1} --db '${database_name}' --add-to-library '$fasta' && - #end if - #end for - kraken2-build --threads \${GALAXY_SLOTS:-1} --db '${database_name}' --build --kmer-len ${kmer_len} --minimizer-len ${minimizer_len} && - cd .. && - python '$__tool_directory__/make_json.py' --db '${database_name}' --out '${out_file}' - ]]> - </command> - <inputs> - <param name="database_name" type="text" label="Name for this database" /> - <param name="libraries" type="select" multiple="true" label="Select partial library to download"> - <option value="archaea">Archaea</option> - <option value="bacteria">Bacteria</option> - <option value="plasmid">Plasmid</option> - <option value="viral">Viral</option> - <option value="human">Human</option> - </param> - <param name="input_fasta" type="data" format="fasta" multiple="True" optional="true" label="Select history item" /> - <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" /> - </inputs> - <outputs> - <data name="out_file" format="data_manager_json" /> - </outputs> - <help> - </help> - <citations> - <citation type="doi">10.1186/gb-2014-15-3-r46</citation> - </citations> -</tool> |
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| diff -r b1805f086b66 -r f9a7275b1cad data_manager/kraken2_standard_database_builder.xml --- a/data_manager/kraken2_standard_database_builder.xml Wed Feb 27 20:42:33 2019 -0500 +++ b/data_manager/kraken2_standard_database_builder.xml Wed Feb 27 20:48:06 2019 -0500 |
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| @@ -1,5 +1,5 @@ <?xml version="1.0"?> -<tool id="kraken2_standard_database_builder" name="Kraken" tool_type="manage_data" version="2.0.7_beta"> +<tool id="kraken2_standard_database_builder" name="Kraken2 Standard Database Builder" tool_type="manage_data" version="2.0.7_beta"> <description>database builder</description> <requirements> <requirement type="package" version="2.0.7_beta">kraken2</requirement> |
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| diff -r b1805f086b66 -r f9a7275b1cad data_manager_conf.xml --- a/data_manager_conf.xml Wed Feb 27 20:42:33 2019 -0500 +++ b/data_manager_conf.xml Wed Feb 27 20:48:06 2019 -0500 |
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| @@ -1,5 +1,20 @@ <data_managers> - <data_manager tool_file="data_manager/kraken2_database_builder.xml" id="kraken2_database_builder" version="1.0"> + <data_manager tool_file="data_manager/kraken2_custom_database_builder.xml" id="kraken2_custom_database_builder" version="1.0"> + <data_table name="kraken2_databases"> + <output> + <column name="value"/> + <column name="name"/> + <column name="path" output_ref="out_file"> + <move type="directory" relativize_symlinks="True"> + <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">kraken2_database/${value}</target> + </move> + <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/kraken2_database/${value}</value_translation> + <value_translation type="function">abspath</value_translation> + </column> + </output> + </data_table> + </data_manager> + <data_manager tool_file="data_manager/kraken2_standard_database_builder.xml" id="kraken2_standard_database_builder" version="1.0"> <data_table name="kraken2_databases"> <output> <column name="value"/> |