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

Adding ctat_cravat_tissues table.

<tool id="ctat_genome_resource_libs_data_manager" 
    name="CTAT Genome Resource Libraries Data Manager" 
    version="2.0.0" tool_type="manage_data">
    <!-- This Data Manager tool was written by Cicada Dennis of Indiana University for the Broad Institute.
    -->
    <description>Retrieve, and/or specify the location of, a CTAT Genome Resource Library. 
    </description>
    <requirements>
        <requirement type="package" version="2.7">python</requirement>
        <requirement type="package" version="0.5.0">fusion-filter</requirement>
        <requirement type="package" version="2.0.1">ctat-mutations</requirement>
    </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
              #end if
              #if str( $genome_resource_library.keep_archive ) == "true":
                --keep_archive
              #end if
              #if str( $genome_resource_library.rebuild ) == "true":
                --new_library_build
              #end if
              #if str( $genome_resource_library.specify_build_location.build_location ) == "true":
                  --build_location="${genome_resource_library.specify_build_location.different_build_location}"
              #end if
            #elif str( $genome_resource_library.build_type ) == "build_from_source":
              --source_location "${genome_resource_library.source_location}"
              #if str( $genome_resource_library.rebuild ) == "true":
                --new_library_build
              #end if
              #if str( $genome_resource_library.specify_build_location.build_location ) == "true":
                  --build_location="${genome_resource_library.specify_build_location.different_build_location}"
              #end if
            #elif str( $genome_resource_library.build_type ) == "specify_built_location":
              --build_location="${genome_resource_library.built_library_location}"
            #end if
            
            #if str( $gmap_options.gmap_build ) == "true":
              --gmap_build 
              #if str( $gmap_options.force_gmap_build ) == "true":
                  --force_gmap_build
              #end if
            #end if
            
            #if str( $mutation_lib_options.mutation_build ) == "true":
              --download_mutation_resources_url="${mutation_lib_options.source_url}" 
              --cosmic_resources_location="${mutation_lib_options.cosmic_files_location}"
              #if str( $mutation_lib_options.force_download ) == "true":
                  --new_mutation_download
              #end if
              #if str( $mutation_lib_options.redo_integration ) == "true":
                  --new_mutation_integration
              #end if
            #end if
        ]]>
    </command>
    <inputs>
        <conditional name="genome_resource_library">
            <param name="build_type" type="select" label="Download CTAT Genome Resource Library?">
                <option value="download_and_build" selected="true">Download from CTAT and build if needed</option>
                <option value="build_from_source">Build library from local source data</option>
                <option value="specify_built_location">Specify location of built library</option>
            </param>
            <when value="download_and_build">
                <!-- The use of a code block to get dynamic options is now deprecated and discouraged.
                     I am still using it here. The only other way I can think of to do this is to
                     create another data_manager that gets the list of files and puts them into a
                     data_table, that is then used to get the filenames. That would require the admin
                     to first run the data_manager that builds the filename data_table before running
                     this data_manager.
                This is the dynamic way to get the options filled.
                <param name="filename" type="select" label="Select File" display="radio" 
                    dynamic_options="get_ctat_genome_urls()" 
                    help="Select a CTAT Genome Resource Library to Download." />
                Here is the static method for what is online in April 2017:
                <param name="filename" type="select" label="Choose which library to download.">
                    <option value="https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/GRCh37_v19_CTAT_lib_Feb092018.plug-n-play.tar.gz">
                        GRCh37_v19_CTAT_lib_Feb092018.plug-n-play.tar.gz
                    </option>
                    <option value="https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/                        GRCh37_v19_CTAT_lib_Feb092018.source_data.tar.gz">
                        GRCh37_v19_CTAT_lib_Feb092018.source_data.tar.gz
                    </option>                        
                    <option value="https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/                        GRCh38_v27_CTAT_lib_Feb092018.plug-n-play.tar.gz">
                        GRCh38_v27_CTAT_lib_Feb092018.plug-n-play.tar.gz
                    </option>
                    <option value="https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/                        GRCh38_v27_CTAT_lib_Feb092018.source_data.tar.gz">
                        GRCh38_v27_CTAT_lib_Feb092018.source_data.tar.gz
                    </option>
                    <option value="https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/                        Mouse_M16_CTAT_lib_Feb202018.plug-n-play.tar.gz">
                        Mouse_M16_CTAT_lib_Feb202018.plug-n-play.tar.gz
                    </option>
                    <option value="https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/                        Mouse_M16_CTAT_lib_Feb202018.source_data.tar.gz">
                        Mouse_M16_CTAT_lib_Feb202018.source_data.tar.gz
                    </option>
                -->
                <param name="download_url" type="select" label="Select a File"
                    dynamic_options="get_ctat_genome_urls()" 
                    help="Select a CTAT Genome Resource Library to Download.">
                </param>
                <param name="download_destination" type="text" label="Download Destination (full path)" />
                <param name="force_new_download" type="boolean" checked="false" label="Force New Download?" />
                <param name="keep_archive" type="boolean" checked="true" label="Keep downloaded archive rather than deleting after build?" />
                <param name="rebuild" type="boolean" checked="false" label="Force new build of Library?" />
                <conditional name="specify_build_location">
                    <param name="build_location" type="boolean" checked="false" label="Is the build location different than the source location?" />
                    <when value="true">
                        <param name="different_build_location" type="text" label="Build Location (full path)" />
                    </when>
                </conditional>
            </when>
            <when value="build_from_source">
                <param name="source_location" type="text" label="Location of Source Files (full path)" />
                <param name="rebuild" type="boolean" checked="false" label="Force new build of Library?" />
                <conditional name="specify_build_location">
                    <param name="build_location" type="boolean" checked="false" label="Is the build location different than the source location?" />
                    <when value="true">
                        <param name="different_build_location" type="text" label="Build Location (full path)" />
                    </when>
                </conditional>
            </when>
            <when value="specify_built_location">
                <param name="built_library_location" type="text" label="Location of the Built Library (full path)" />
            </when>
        </conditional>
        <param name="display_name" type="text" label="Reference Genome Display Name" />
        <conditional name="gmap_options">
            <param name="gmap_build" type="boolean" checked="true" label="Do a gmap_build on the Library?" />
            <when value="true">
                <param name="force_gmap_build" type="boolean" checked="false" label="Force a new build even if previously done?" />
            </when>
        </conditional>
        <conditional name="mutation_lib_options">
            <param name="mutation_build" type="boolean" checked="false" label="Download and integrate mutation library?">
            </param>
            <when value="true">
                <param name="source_url" type="select" label="Select a File"
                    dynamic_options="get_mutation_resource_urls()" 
                    help="Select CTAT Mutation Library File to Download.\nMake sure it is the right one for your CTAT Genome Resource Library!">
                </param>
                <param name="force_download" type="boolean" checked="false" label="Force New Download?" />
                <param name="redo_integration" type="boolean" checked="false" label="Redo Library Integration?" />
                <param name="cosmic_files_location" type="text" label="Location of the COSMIC files (See Tool Notes)." />
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data name="out_file" format="data_manager_json" />
    </outputs>
    <help>
        Retrieve, and/or specify the location of, a CTAT Genome Resource Library.
        
        There are three options: 1) Download from CTAT and build if needed; 2) Build library from local source data; 3) Specify location of built library.
        
        1) Download from CTAT and build if needed: 
           This option uses the files at https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/
           as selectors for the user to choose among.
           Specify the Full Path of the location where the CTAT Genome Resource Library should be placed.
           The other options should be self-explanatory.
        2) Build library from local source data:
           This assumes that you have already downloaded the source data for a build and you want to build it.
        3) Specify location of built library:
           This assumes you already have a build library and need tell galaxy where it is.

        All options allow the user to do a gmap_build on the library 
        and also to integrate ctat-mutation resources into the library.

        You will need approximately 62GB of space for a human genome resource library, once it is built, 
        but if downloading and building, to be safe provide at least 75GB.

        The installation of this tool takes some time, due to building a conda environment for the dependencies.
        The "source_data" files download faster, but then must be built.
        Building the library from the "source_data" files can take many hours, depending on the resources of your machine.
        The "plug-n-play" can take considerable time to download, depending on your internet connection. Even with high speed,
        it is about 25GB that is transfered, so plan accordingly.
        If you have a good speed internet connection, downloading the plug-n-play will usually be faster than building.

        **If a download or a build is interrupted, re-running the job should pick up where it left off.**

        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 
        integrated into the Library. 

        The Mouse genome is not currently supported by ctat_mutations.

        If the Reference Genome Display Name is left empty a name will be created, 
        but any text that will best guide the user can be entered here. 
        It will be the text that is used for selecting the library in pull down lists 
        requiring a Genome Reference Library resource (These are stored in the ctat_genome_resource_libs table).

        For more information on CTAT Genome Resource Libraries, 
        see https://github.com/FusionFilter/FusionFilter/wiki
    </help>
    <code file="add_ctat_resource_lib.py" />
</tool>