Mercurial > repos > sanbi-uwc > data_manager_fetch_refseq

view data_manager_conf.xml @ 13:dd9f976e9d97 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/pvanheus/refseq_fasta_data_manager commit 687fed3e6ffed745baf5d6241ee82f2bd9671256-dirty
author sanbi-uwc
date Sat, 08 Sep 2018 03:08:02 -0400
parents 97bf61f2fdae
children 1977080c99ec
line wrap: on
line source

<?xml version="1.0"?>
<data_managers>    
    <data_manager tool_file="data_manager/fetch_refseq.xml" id="fetch_genome_fetch_refseq">
        <data_table name="all_fasta">
            <output>
                <column name="value" />
                <column name="dbkey" />
                <column name="name" />
                <column name="path" output_ref="output_file" >
                    <move type="file">
                        <source>${path}</source>
                        <target base="${GALAXY_DATA_MANAGER_DATA_PATH}"><![CDATA[
                        #set release_num = str($dbkey).split()[1]                        
                        refseq/${release_num}/${value}.fasta
                        ]]></target>
                    </move>
                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/refseq/${dbkey}/${value}.fasta</value_translation>
                    <value_translation type="function">abspath</value_translation>
                </column>
            </output>
        </data_table>
    </data_manager>    
</data_managers>