comparison data_manager/data_manager_eggnog.xml @ 3:9d94fe7ce8b9 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit e711920c41c8862d7d8133f7b455cf475924e103

2:a74d61dbd155

<tool id="data_manager_eggnog" name="EggNOG DB Download" version="@VERSION@" tool_type="manage_data">
    <description>Download a new database</description>
    <macros>
        <token name="@VERSION@">4.5.1</token>
    </macros>
    <requirements>
        <requirement type="package" version="@VERSION@">eggnog-mapper</requirement>
    </requirements>
    <version_command>emapper.py --version</version_command>
    <command detect_errors="exit_code"><![CDATA[
#import json, os
#set params = json.loads(open(str($out_file)).read())
#set install_path = $params['output_data'][0]['extra_files_path'].encode('ascii', 'replace')
#if $dbs:
#set $eggnogdbs = ' '.join($dbs.split(','))
#else
#set $eggnogdbs = 'none'
#endif
#if $test == 'false'
mkdir -p '${target_directory}' &&
download_eggnog_data.py 
  $diamond_database -y -q --data_dir $install_path $eggnogdbs
' '.join(dbs.split(',')) &&
#end if
python '${__tool_directory__}/data_manager_eggnog.py --config_file $out_file --install_path $target_directory --dbs '$dbs'
    ]]></command>
    <inputs>
        <param name="test" type="hidden" value="false" />
        <param name="target_path" type="text" label="Download Destination (full path)" />
        <param name="diamond_database" type="boolean" truevalue="" falsevalue="-D" checked="true" label="Install the diamond database"/>

        </test>
    </tests>
    <help><![CDATA[
This tool downloads eggnog data using download_eggnog_data.py 
and populates the data tables: eggnog_mapper_db and eggnog_mapper_hmm_dbs.
    ]]></help>
    <citations>
        <citation type="doi">10.1093/nar/gkv1248</citation>
    </citations>
</tool>

3:9d94fe7ce8b9

<tool id="data_manager_eggnog" name="EggNOG DB Download" version="@VERSION@.0" tool_type="manage_data">
    <description>Download a new database</description>
    <macros>
        <token name="@VERSION@">1.0.3</token>
    </macros>
    <requirements>
        <requirement type="package" version="@VERSION@">eggnog-mapper</requirement>
    </requirements>
    <version_command>emapper.py --version</version_command>
    <command detect_errors="exit_code"><![CDATA[
#import json, os
#set params = json.loads(open(str($out_file)).read())
#set install_path = $params['output_data'][0]['extra_files_path'].encode('ascii', 'replace')
#if $dbs:
#set $eggnogdbs = ' '.join(str($dbs).split(','))
#else
#set $eggnogdbs = 'none'
#end if
#if $test == 'false'
mkdir -p '${install_path}' &&
download_eggnog_data.py 
  $diamond_database -y -q --data_dir $install_path $eggnogdbs
' '.join(dbs.split(',')) &&
#else
#set $install_path = '/Users/jj/gx/gh/jj/tools-galaxyp/tools/eggnog_mapper/test-data/cached_locally'
#end if
python '${__tool_directory__}/data_manager_eggnog.py' --config_file '$out_file' --install_path '$install_path' --dbs '$dbs'
    ]]></command>
    <inputs>
        <param name="test" type="hidden" value="false" />
        <param name="target_path" type="text" label="Download Destination (full path)" />
        <param name="diamond_database" type="boolean" truevalue="" falsevalue="-D" checked="true" label="Install the diamond database"/>

        </test>
    </tests>
    <help><![CDATA[
This tool downloads eggnog data using download_eggnog_data.py 
and populates the data tables: eggnog_mapper_db and eggnog_mapper_hmm_dbs.
The data is located at: http://eggnogdb.embl.de/download/emapperdb-4.5.1/
The optional eggNOG HMM databases: http://eggnogdb.embl.de/download/emapperdb-4.5.1/hmmdb_levels/ 
can vary from 1G to 80G in size.
    ]]></help>
    <citations>
        <citation type="doi">10.1093/nar/gkv1248</citation>
    </citations>
</tool>