Commit 424fae37 authored by Evan Bolyen's avatar Evan Bolyen
Browse files

Fix softlink of q2view display_app

parent fd1b0910

config/tool_data_table_conf.xml.sample

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<!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changed in revision 4550:535d276c92bc-->

<tables>

    <!-- Locations of all fasta files under genome directory -->

    <table name="all_fasta" comment_char="#" allow_duplicate_entries="False">

        <columns>value, dbkey, name, path</columns>

        <file path="tool-data/all_fasta.loc" />

    </table>

    <!-- Locations of indexes in the BFAST mapper format -->

    <table name="bfast_indexes" comment_char="#" allow_duplicate_entries="False">

        <columns>value, dbkey, formats, name, path</columns>

        <file path="tool-data/bfast_indexes.loc" />

    </table>

    <!-- Locations of nucleotide BLAST databases -->

    <table name="blastdb" comment_char="#" allow_duplicate_entries="False">

        <columns>value, name, path</columns>

        <file path="tool-data/blastdb.loc" />

    </table>

    <!-- Locations of protein BLAST databases -->

    <table name="blastdb_p" comment_char="#" allow_duplicate_entries="False">

        <columns>value, name, path</columns>

        <file path="tool-data/blastdb_p.loc" />

    </table>

    <!-- Locations of protein domain BLAST databases -->

    <table name="blastdb_d" comment_char="#" allow_duplicate_entries="False">

        <columns>value, name, path</columns>

        <file path="tool-data/blastdb_d.loc" />

    </table>

    <!-- Locations of indexes in the BWA mapper format -->

    <table name="bwa_indexes" comment_char="#" allow_duplicate_entries="False">

        <columns>value, dbkey, name, path</columns>

        <file path="tool-data/bwa_index.loc" />

    </table>

    <!-- Locations of indexes in the BWA color-space mapper format -->

    <table name="bwa_indexes_color" comment_char="#" allow_duplicate_entries="False">

        <columns>value, dbkey, name, path</columns>

        <file path="tool-data/bwa_index_color.loc" />

    </table>

    <!-- Locations of MAF files that have been indexed with bx-python -->

    <table name="indexed_maf_files">

        <columns>name, value, dbkey, species</columns>

        <file path="tool-data/maf_index.loc" />

    </table>

    <!-- Locations of fasta files appropriate for NGS simulation -->

    <table name="ngs_sim_fasta" comment_char="#" allow_duplicate_entries="False">

        <columns>value, dbkey, name, path</columns>

        <file path="tool-data/ngs_sim_fasta.loc" />

    </table>

    <!-- Locations of PerM base index files -->

    <table name="perm_base_indexes" comment_char="#" allow_duplicate_entries="False">

        <columns>value, name, path</columns>

        <file path="tool-data/perm_base_index.loc" />

    </table>

    <!-- Locations of PerM color-space index files -->

    <table name="perm_color_indexes" comment_char="#" allow_duplicate_entries="False">

        <columns>value, name, path</columns>

        <file path="tool-data/perm_color_index.loc" />

    </table>

    <!-- Location of Picard dict file and other files -->

    <table name="picard_indexes" comment_char="#" allow_duplicate_entries="False">

        <columns>value, dbkey, name, path</columns>

        <file path="tool-data/picard_index.loc" />

    </table>

    <!-- Location of SRMA dict file and other files -->

    <table name="srma_indexes" comment_char="#" allow_duplicate_entries="False">

        <columns>value, dbkey, name, path</columns>

        <file path="tool-data/picard_index.loc" />

    </table>

    <!-- Location of Mosaik files -->

    <table name="mosaik_indexes" comment_char="#" allow_duplicate_entries="False">

        <columns>value, dbkey, name, path</columns>

        <file path="tool-data/mosaik_index.loc" />

    </table>

    <!-- Locations of indexes in the 2bit format -->

    <table name="twobit" comment_char="#" allow_duplicate_entries="False">

        <columns>value, path</columns>

        <file path="tool-data/twobit.loc" />

    </table>

    <!-- Available IGV builds, loaded from URL -->

    <table name="igv_broad_genomes" comment_char="#" allow_duplicate_entries="False">

        <columns>name, url, value</columns>

        <file url="http://igv.broadinstitute.org/genomes/genomes.txt" />

    </table>

    <!-- Available liftOver chain file -->

    <table name="liftOver" comment_char="#" allow_duplicate_entries="False">

        <columns>dbkey, name, value</columns>

        <file path="tool-data/liftOver.loc" />

    </table>

    <!-- iobio bam servers -->

    <table name="bam_iobio" comment_char="#" allow_duplicate_entries="False">

        <columns>value, name, url</columns>

        <file path="tool-data/bam_iobio.loc" />

    </table>

    <!-- iobio vcf servers -->

    <table name="vcf_iobio" comment_char="#" allow_duplicate_entries="False">

        <columns>value, name, url</columns>

        <file path="tool-data/vcf_iobio.loc" />

    </table>

    <!-- simple biom servers -->

    <table name="biom_simple_display" comment_char="#" allow_duplicate_entries="False">

        <columns>value, name, url</columns>

        <file path="tool-data/biom_simple_display.loc" />

    </table>

    <!-- simple intermine servers -->

    <table name="intermine_simple_display" comment_char="#" allow_duplicate_entries="False">

        <columns>value, name, url</columns>

        <file path="tool-data/intermine_simple_display.loc" />

    </table>

    <!-- q2view servers -->

    <table name="q2view_display" comment_char="#" allow_duplicate_entries="False">

        <columns>value, name, url</columns>

        <file path="tool-data/q2view_display.loc" />

    </table>

</tables>

config/tool_data_table_conf.xml.sample

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../lib/galaxy/config/sample/tool_data_table_conf.xml.sample
 
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lib/galaxy/config/sample/tool_data_table_conf.xml.sample

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@@ -157,4 +157,9 @@ 
        <field name="name" template="true">${__REFGENIE_DISPLAY_NAME__}</field>

        <field name="path" template="true">${__REFGENIE_ASSET__}</field>

    </table>

    <!-- q2view servers -->

    <table name="q2view_display" comment_char="#" allow_duplicate_entries="False">

        <columns>value, name, url</columns>

        <file path="tool-data/q2view_display.loc" />

    </table>

</tables>

config/tool_data_table_conf.xml.sample

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File changed.File mode changed from 100644 to 120000.

Contains only whitespace changes.