Mercurial > repos > proteore > proteore_data_manager

view data_manager_conf.xml @ 5:b05fa99ddda2 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload commit a23ff40d482d58e0425108bf60372e5fcafb847e"
author proteore
date Thu, 06 Feb 2020 04:02:50 -0500
parents e967a99d66b3
children
line wrap: on
line source

<?xml version="1.0"?>
<data_managers>
    <data_manager tool_file="data_manager/resource_building.xml" id="resource_building">
        <data_table name="proteore_peptide_atlas">
            <output>
                <column name="id"/>
                <column name="name" />
                <column name="tissue" />
                <column name="value" output_ref="output" >
                    <move type="file">
                        <!--source>${path}/${value}.tsv</source-->
                        <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">peptide_atlas/</target>
                    </move>
                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/peptide_atlas/${id}.tsv</value_translation>
                    <value_translation type="function">abspath</value_translation>
                </column>
            </output>
        </data_table>
        <data_table name="proteore_protein_atlas_normal_tissue">
            <output>
                <column name="id"/>
                <column name="release"/>
                <column name="name" />
                <column name="tissue" />
                <column name="value" output_ref="output" >
                    <move type="file">
                        <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">protein_atlas/</target>
                    </move>
                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/protein_atlas/${release}.tsv</value_translation>
                    <value_translation type="function">abspath</value_translation>
                </column>
            </output>
        </data_table>
        <data_table name="proteore_protein_atlas_rna_tissue">
            <output>
                <column name="id"/>
                <column name="release"/>
                <column name="name" />
                <column name="tissue" />
                <column name="value" output_ref="output" >
                    <move type="file">
                        <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">protein_atlas/</target>
                    </move>
                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/protein_atlas/${release}.tsv</value_translation>
                    <value_translation type="function">abspath</value_translation>
                </column>
            </output>
        </data_table>
        <data_table name="proteore_protein_atlas_tumor_tissue">
            <output>
                <column name="id"/>
                <column name="release"/>
                <column name="name" />
                <column name="tissue" />
                <column name="value" output_ref="output" >
                    <move type="file">
                        <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">protein_atlas/</target>
                    </move>
                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/protein_atlas/${release}.tsv</value_translation>
                    <value_translation type="function">abspath</value_translation>
                </column>
            </output>
        </data_table>
        <data_table name="proteore_protein_full_atlas">
            <output>
                <column name="id"/>
                <column name="release"/>
                <column name="name" />
                <column name="tissue" />
                <column name="value" output_ref="output" >
                    <move type="file">
                        <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">protein_atlas/</target>
                    </move>
                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/protein_atlas/${release}.tsv</value_translation>
                    <value_translation type="function">abspath</value_translation>
                </column>
            </output>
        </data_table>
        <data_table name="proteore_id_mapping_Human">
            <output>
                <column name="id" />
                <column name="release"/>
                <column name="name" />
                <column name="species" />
                <column name="value" output_ref="output" >
                    <move type="file">
                        <!--source>${path}</source-->
                        <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">id_mapping/</target>
                    </move>
                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/id_mapping/${release}.tsv</value_translation>
                    <value_translation type="function">abspath</value_translation>
                </column>
            </output>
        </data_table>
        <data_table name="proteore_id_mapping_Mouse">
            <output>
                <column name="id" />
                <column name="release"/>
                <column name="name" />
                <column name="species" />
                <column name="value" output_ref="output" >
                    <move type="file">
                        <!--source>${path}</source-->
                        <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">id_mapping/</target>
                    </move>
                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/id_mapping/${release}.tsv</value_translation>
                    <value_translation type="function">abspath</value_translation>
                </column>
            </output>
        </data_table>
        <data_table name="proteore_id_mapping_Rat">
            <output>
                <column name="id" />
                <column name="release"/>
                <column name="name" />
                <column name="species" />
                <column name="value" output_ref="output" >
                    <move type="file">
                        <!--source>${path}</source-->
                        <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">id_mapping/</target>
                    </move>
                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/id_mapping/${release}.tsv</value_translation>
                    <value_translation type="function">abspath</value_translation>
                </column>
            </output>
        </data_table>
        <data_table name="proteore_biogrid_dictionaries">
            <output>
                <column name="id" />
                <column name="release"/>
                <column name="name" />
                <column name="species" />
                <column name="value" output_ref="output" >
                    <move type="file">
                        <!--source>${path}</source-->
                        <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">PPI_dictionaries/</target>
                    </move>
                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/PPI_dictionaries/${release}.json</value_translation>
                    <value_translation type="function">abspath</value_translation>
                </column>
            </output>
        </data_table>
        <data_table name="proteore_bioplex_dictionaries">
            <output>
                <column name="id" />
                <column name="release"/>
                <column name="name" />
                <column name="species" />
                <column name="value" output_ref="output" >
                    <move type="file">
                        <!--source>${path}</source-->
                        <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">PPI_dictionaries/</target>
                    </move>
                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/PPI_dictionaries/${release}.json</value_translation>
                    <value_translation type="function">abspath</value_translation>
                </column>
            </output>
        </data_table>
        <data_table name="proteore_humap_dictionaries">
            <output>
                <column name="id" />
                <column name="release"/>
                <column name="name" />
                <column name="species" />
                <column name="value" output_ref="output" >
                    <move type="file">
                        <!--source>${path}</source-->
                        <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">PPI_dictionaries/</target>
                    </move>
                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/PPI_dictionaries/${release}.json</value_translation>
                    <value_translation type="function">abspath</value_translation>
                </column>
            </output>
        </data_table>
        <data_table name="proteore_nextprot_ref">
            <output>
                <column name="id" />
                <column name="release"/>
                <column name="name" />
                <column name="value" output_ref="output" >
                    <move type="file">
                        <!--source>${path}</source-->
                        <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">proteore_nextprot_ref/</target>
                    </move>
                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/proteore_nextprot_ref/${release}.tsv</value_translation>
                    <value_translation type="function">abspath</value_translation>
                </column>
            </output>
        </data_table>
    </data_manager>
</data_managers>