comparison data_manager/add_ctat_resource_lib.xml @ 52:0e3e4f24e300 draft

Adding ctat_cravat_tissues table.

51:0a4bec29a609

    </requirements>
    <command detect_errors="exit_code">
        <![CDATA[
          python $__tool_directory__/add_ctat_resource_lib.py 
            --output_filename="${out_file}" 
            --display_name="${display_name}"            
            #if str( $genome_resource_library.build_type ) == "download_and_build":
              --download_url="${genome_resource_library.download_url}" 
              --download_location="${genome_resource_library.download_destination}"
              #if str( $genome_resource_library.force_new_download ) == "true":
                --new_archive_download

        Neither the "source_data" nor the "plug-n-play" versions have had their gmap index built. If you are not going to be
        using gmap_fusion, then you can uncheck the gmap_build check box and save the space and time building the index consumes.

        Neither the "source_data" nor the "plug-n-play" versions have Mutation Resources included. 
        Those must be downloaded separately and integrated into the Library. If you are going to be using the 
        ctat_mutations tool, check the Download Mutation Library check box.

        In order to integrate the Mutation Resources into a CTAT Genome Resource Library, you must have previously downloaded
        COSMIC resources (See Step 2 from https://github.com/NCIP/ctat-mutations/tree/master/mutation_lib_prep )
        You can place them directly into the Genome Resource Library location, or if the Library is 
        not built yet, or you do not know the full path to it, specify the directory where the COSMIC files are, so they can be 

52:0e3e4f24e300

    </requirements>
    <command detect_errors="exit_code">
        <![CDATA[
          python $__tool_directory__/add_ctat_resource_lib.py 
            --output_filename="${out_file}" 
            --display_name="${display_name}"
            --cravat_tissues_filepath="${__tool_directory__}/../tool-data/ctat_cravat_tissues.loc.sample"           
            #if str( $genome_resource_library.build_type ) == "download_and_build":
              --download_url="${genome_resource_library.download_url}" 
              --download_location="${genome_resource_library.download_destination}"
              #if str( $genome_resource_library.force_new_download ) == "true":
                --new_archive_download

        Neither the "source_data" nor the "plug-n-play" versions have had their gmap index built. If you are not going to be
        using gmap_fusion, then you can uncheck the gmap_build check box and save the space and time building the index consumes.

        Neither the "source_data" nor the "plug-n-play" versions have Mutation Resources included. 
        Those must be downloaded separately and integrated into the Library. If you are going to be using the 
        ctat_mutations tool, check the Download Mutation Library check box. Whether or not you check this box, the
        ctat_cravat_tissues table needed by the ctat_mutations tool will be created.

        In order to integrate the Mutation Resources into a CTAT Genome Resource Library, you must have previously downloaded
        COSMIC resources (See Step 2 from https://github.com/NCIP/ctat-mutations/tree/master/mutation_lib_prep )
        You can place them directly into the Genome Resource Library location, or if the Library is 
        not built yet, or you do not know the full path to it, specify the directory where the COSMIC files are, so they can be