annotate data_manager/data_manager_sylph_database.xml @ 0:130224fe2d18 draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_sylph_database commit 6ac2834ca0a21512c9986e2fb8d0dcda1c4b0e18

<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>