Mercurial > repos > trinity_ctat > ctat_genome_resource_libs_data_manager_3
diff data_manager/add_ctat_resource_lib.xml @ 44:76f2367996b8 draft
Uploaded
| author | trinity_ctat |
|---|---|
| date | Thu, 25 Oct 2018 17:30:36 -0400 |
| parents | |
| children | c47ac2deaaf8 |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager/add_ctat_resource_lib.xml Thu Oct 25 17:30:36 2018 -0400 @@ -0,0 +1,219 @@ +<tool id="ctat_genome_resource_libs_data_manager" + name="CTAT Genome Resource Libraries Data Manager" + version="2.0.0" tool_type="manage_data"> + <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}" + #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> + <!-- The following are left in here, just as examples of various ways of doing options. + <param name="force_download" type="boolean" checked="false" + truevalue="- -force_download" falsevalue="" label="Force New Download? (yes/no)" /> + <param name="download" type="select" label="Need to Download?"> + <option value="single" selected="true">Single Dataset</option> + <option value="paired_collection">Paired Collection</option> + <when value="paired_collection"> + <param name="fastq_input" format="fastqsanger" type="data_collection" collection_type="paired" label="Select dataset pair" help="Specify paired dataset collection containing paired reads"/> + </when> + --> + <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_filenames()" + 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 this 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. By default the Mutation Resources are not 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 + 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 (ctat_genome_resource_libs). + + For more information on CTAT Genome Resource Libraries, + see https://github.com/FusionFilter/FusionFilter/wiki + </help> + <code file="add_ctat_resource_lib.py" /> +</tool>