Mercurial > repos > bgruening > data_manager_sylph_database
changeset 0:2ea34d422df4 draft default tip
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_sylph_database commit 6ac2834ca0a21512c9986e2fb8d0dcda1c4b0e18
| author | bgruening |
|---|---|
| date | Fri, 23 May 2025 09:47:40 +0000 |
| parents | |
| children | |
| files | data_manager/data_manager_sylph_database.xml data_manager_conf.xml test-data/sylph_databases.loc.test tool-data/sylph_databases.loc.sample tool_data_table_conf.xml.sample tool_data_table_conf.xml.test |
| diffstat | 6 files changed, 221 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager/data_manager_sylph_database.xml Fri May 23 09:47:40 2025 +0000 @@ -0,0 +1,165 @@ +<tool id="data_manager_sylph_database" name="Download pre-built sylph databases" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" tool_type="manage_data" profile="@PROFILE@"> + <description></description> + <macros> + <token name="@TOOL_VERSION@">0.8.1</token> + <token name="@VERSION_SUFFIX@">0</token> + <token name="@PROFILE@">23.0</token> + <token name="@DB_VERSION@">1</token> + </macros> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">sylph</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + +#set $file = str($db_link).split('/')[-1] + +mkdir -p '$out_file.extra_files_path' && +wget $db_link && +mv '$file' '$out_file.extra_files_path' && +cp '$dmjson' '$out_file' + ]]></command> + <configfiles> + <configfile name="dmjson"><![CDATA[ +#from datetime import date +#set $file = str($db_link).split('/')[-1] + +{ + "data_tables":{ + "sylph_databases":[ + { + "value": "sylph_downloaded_#echo date.today().strftime('%d%m%Y')#_${file}", + "name": "sylph database ${file}", + "path": "${file}", + "clade": "${clades}", + "sylph_tax_identifier": "${name}", + "version": "@DB_VERSION@" + } + ] +} + }]]></configfile> + </configfiles> + <inputs> + <conditional name="db_type"> + <param argument="clades" type="select" label="Type of Databases"> + <option value="prokaryote">Prokaryote databases</option> + <option value="eukaryote">Eukaryote databases</option> + <option value="virus">Virus databases</option> + </param> + <when value="prokaryote"> + <conditional name="db_name"> + <param argument="name" type="select" label="Database"> + <option value="GTDB_r220">GTDB r220</option> + <option value="GTDB_r214">GTDB r214</option> + <option value="OceanDNA">Ocean DNA</option> + <option value="SoilSMAG">Soil MAGs</option> + </param> + <when value="GTDB_r220"> + <param name="db_link" type="select" label="Sylph prokaryote databases"> + <option value="http://faust.compbio.cs.cmu.edu/sylph-stuff/gtdb-r220-c200-dbv1.syldb" selected="true">GTDB-r220 (April 2024) -c 200, more sensitive database</option> + <option value="http://faust.compbio.cs.cmu.edu/sylph-stuff/gtdb-r220-c1000-dbv1.syldb">GTDB-r220 (April 2024) -c 1000 more efficient, less sensitive database</option> + </param> + </when> + <when value="GTDB_r214"> + <param name="db_link" type="select" label="Sylph prokaryote databases"> + <option value="http://faust.compbio.cs.cmu.edu/sylph-stuff/v0.3-c200-gtdb-r214.syldb">GTDB-r214 (April 2023) -c 200, more sensitive database</option> + <option value="http://faust.compbio.cs.cmu.edu/sylph-stuff/v0.3-c1000-gtdb-r214.syldb">GTDB-r214 (April 2023) -c 1000 more efficient, less sensitive database</option> + </param> + </when> + <when value="OceanDNA"> + <param name="db_link" type="select" label="Sylph prokaryote databases"> + <option value="http://faust.compbio.cs.cmu.edu/sylph-stuff/OceanDNA-c200-v0.3.syldb">OceanDNA - ocean MAGs from Nishimura and Yoshizawa, -c 200, more sensitive database</option> + </param> + </when> + <when value="SoilSMAG"> + <param name="db_link" type="select" label="Sylph prokaryote databases"> + <option value="http://faust.compbio.cs.cmu.edu/sylph-stuff/SMAG-c200-v0.3.syldb">SoilSMAG (SMAG) from Ma et al. -c 200, more sensitive database</option> + </param> + </when> + </conditional> + </when> + <when value="eukaryote"> + <conditional name="db_name"> + <param argument="name" type="select" label="Database"> + <option value="FungiRefSeq-2024-07-25">Refseq fungi 2024-07-25</option> + <option value="TaraEukaryoticSMAG">TARA eukaryotic SMAGs</option> + </param> + <when value="FungiRefSeq-2024-07-25"> + <param name="db_link" type="select" label="Sylph eukaryote databases"> + <option value="http://faust.compbio.cs.cmu.edu/sylph-stuff/fungi-refseq-2024-07-25-c200-v0.3.syldb" selected="true">FungiRefSeq-2024-07-25 - Refseq fungi representative genomes collected on 2024-07-25</option> + </param> + </when> + <when value="TaraEukaryoticSMAG"> + <param name="db_link" type="select" label="Sylph eukaryote databases"> + <option value="http://faust.compbio.cs.cmu.edu/sylph-stuff/tara-eukmags-c200-v0.3.syldb">TaraEukaryoticSMAG - TARA eukaryotic SMAGs from Delmont et al. -c 200, more sensitive database</option> + </param> + </when> + </conditional> + </when> + <when value="virus"> + <conditional name="db_name"> + <param argument="name" type="select" label="Database"> + <option value="IMGVR_4.1">IMG/VR 4.1</option> + </param> + <when value="IMGVR_4.1"> + <param name="db_link" type="select" label="Sylph virus databases"> + <option value="http://faust.compbio.cs.cmu.edu/sylph-stuff/imgvr_c200_v0.3.0.syldb" selected="true">IMGVR_4.1 high-confidence viral OTU genomes, -c 200, more sensitive database</option> + </param> + </when> + </conditional> + </when> + </conditional> + </inputs> + <outputs> + <data name="out_file" format="data_manager_json" label="${tool.name}"/> + </outputs> + <tests> + <test expect_num_outputs="1"> + <conditional name="db_type"> + <param name="clades" value="eukaryote"/> + <conditional name="db_name"> + <param name="name" value="FungiRefSeq-2024-07-25"/> + <param name="db_link" value="http://faust.compbio.cs.cmu.edu/sylph-stuff/fungi-refseq-2024-07-25-c200-v0.3.syldb"/> + </conditional> + </conditional> + <output name="out_file"> + <assert_contents> + <has_text text='"sylph_databases":'/> + <has_text_matching expression='"value": "sylph_downloaded_[0-9]{8}_fungi-refseq-2024-07-25-c200-v0.3.syldb"'/> + <has_text text='"name": "sylph database fungi-refseq-2024-07-25-c200-v0.3.syldb"'/> + <has_text_matching expression='"path": "fungi-refseq-2024-07-25-c200-v0.3.syldb"'/> + <has_text text='"clade": "eukaryote"'/> + <has_text text='"sylph_tax_identifier": "FungiRefSeq-2024-07-25"'/> + <has_text text='"version": "@DB_VERSION@"'/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="1"> + <conditional name="db_type"> + <param name="clades" value="prokaryote"/> + <conditional name="db_name"> + <param name="name" value="OceanDNA"/> + <param name="db_link" value="http://faust.compbio.cs.cmu.edu/sylph-stuff/OceanDNA-c200-v0.3.syldb"/> + </conditional> + </conditional> + <output name="out_file"> + <assert_contents> + <has_text text='"sylph_databases":'/> + <has_text_matching expression='"value": "sylph_downloaded_[0-9]{8}_OceanDNA-c200-v0.3.syldb"'/> + <has_text text='"name": "sylph database OceanDNA-c200-v0.3.syldb"'/> + <has_text_matching expression='"path": "OceanDNA-c200-v0.3.syldb"'/> + <has_text text='"clade": "prokaryote"'/> + <has_text text='"sylph_tax_identifier": "OceanDNA"'/> + <has_text text='"version": "@DB_VERSION@"'/> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ +This tool downloads pre-built sylph databases. +-c: the compression parameter. Memory/runtime scale like 1/c; higher c is faster but less sensitive at low coverage. +Default c = 200. The -c for genomes must be than sup or = the -c for reads (strict sup is allowed) + ]]></help> + <citations> + <citation type="doi">10.1038/s41587-024-02412-y</citation> + </citations> +</tool> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager_conf.xml Fri May 23 09:47:40 2025 +0000 @@ -0,0 +1,22 @@ +<?xml version="1.0"?> +<data_managers> + <data_manager tool_file="data_manager/data_manager_sylph_database.xml" id="data_manager_sylph_database"> + <data_table name="sylph_databases"> <!-- 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 --> + <column name="path" output_ref="out_file"> + <move type="file"> + <source>${path}</source> + <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">sylph/${path}</target> + </move> + <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/sylph/${path}</value_translation> + <value_translation type="function">abspath</value_translation> + </column> + <column name="clade"/> + <column name="sylph_tax_identifier"/> + <column name="version"/> + </output> + </data_table> + </data_manager> +</data_managers> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sylph_databases.loc.test Fri May 23 09:47:40 2025 +0000 @@ -0,0 +1,12 @@ +#This is a tab separated file describing the location of StarAMR databases +#used for the StarAMR tool +# +#file has this format (white space characters are TAB characters) +# +#The columns are: +#value name path version +# +#For example +#staramr_downloaded_20241004_resfinder_d1e607b_pointfinder_694919f_plasmidfinder_3e77502 ResFinder: tag 4.6.0, commit d1e607b, 2024-08-06 - PointFinder: tag 4.1.1, commit 694919f, 2024-08-08 - PlasmidFinder: commit 3e77502, 2024-03-07 (downloaded 20241004) /path/to/data +sylph_downloaded_22052025_fungi-refseq-2024-07-25-c200-v0.3.syldb sylph database fungi-refseq-2024-07-25-c200-v0.3.syldb /tmp/tmpwo1n9334/galaxy-dev/tool-data/sylph/fungi-refseq-2024-07-25-c200-v0.3.syldb eukaryote FungiRefSeq-2024-07-25 1 +sylph_downloaded_22052025_OceanDNA-c200-v0.3.syldb sylph database OceanDNA-c200-v0.3.syldb /tmp/tmpwo1n9334/galaxy-dev/tool-data/sylph/OceanDNA-c200-v0.3.syldb prokaryote OceanDNA 1
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/sylph_databases.loc.sample Fri May 23 09:47:40 2025 +0000 @@ -0,0 +1,10 @@ +#This is a tab separated file describing the location of StarAMR databases +#used for the StarAMR tool +# +#file has this format (white space characters are TAB characters) +# +#The columns are: +#value name path version +# +#For example +#staramr_downloaded_20241004_resfinder_d1e607b_pointfinder_694919f_plasmidfinder_3e77502 ResFinder: tag 4.6.0, commit d1e607b, 2024-08-06 - PointFinder: tag 4.1.1, commit 694919f, 2024-08-08 - PlasmidFinder: commit 3e77502, 2024-03-07 (downloaded 20241004) /path/to/data \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Fri May 23 09:47:40 2025 +0000 @@ -0,0 +1,6 @@ +<tables> + <table name="sylph_databases" comment_char="#"> + <columns>value, name, path, clade, sylph_tax_identifier, version</columns> + <file path="tool-data/sylph_databases.loc"/> + </table> +</tables> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Fri May 23 09:47:40 2025 +0000 @@ -0,0 +1,6 @@ +<tables> + <table name="sylph_databases" comment_char="#"> + <columns>value, name, path, clade, sylph_tax_identifier, version</columns> + <file path="${__HERE__}/test-data/sylph_databases.loc.test"/> + </table> +</tables> \ No newline at end of file