Mercurial > repos > trinity_ctat > ctat_genome_resource_libs_data_manager_3
annotate data_manager/add_ctat_resource_lib.xml @ 20:cf8155c24783 draft
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| author | trinity_ctat |
|---|---|
| date | Fri, 19 Oct 2018 17:57:46 -0400 |
| parents | 99acaf768ed4 |
| children | f403d561cda9 |
| rev | line source |
|---|---|
| 1 | 1 <tool id="ctat_genome_resource_libs_data_manager" |
| 2 name="CTAT Genome Resource Libraries Data Manager" | |
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3 version="2.0.0" tool_type="manage_data"> |
| 0 | 4 <description>Retrieve, and/or specify the location of, a CTAT Genome Resource Library. |
| 5 </description> | |
| 6 <requirements> | |
| 7 <requirement type="package" version="2.7">python</requirement> | |
| 8 <requirement type="package" version="0.5.0">fusion-filter</requirement> | |
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9 <requirement type="package" version="2.0.1">ctat-mutations</requirement> |
| 0 | 10 </requirements> |
| 11 <command detect_errors="default"> | |
| 12 <![CDATA[ | |
| 10 | 13 python $__tool_directory__/add_ctat_resource_lib.py |
| 14 --output_filename="${out_file}" | |
| 15 --display_name="${display_name}" | |
| 16 | 16 #if str($genome_resource_library.build_type) == "build_from_source": |
| 17 --source_location "${genome_resource_library.source_location}" | |
| 18 #if str($genome_resource_library.rebuild) == "true": | |
| 19 --new_library_build | |
| 20 #end if | |
| 20 | 21 if str($specify_build_location.build_location) == "true": |
| 22 --build_location="${specify_build_location.different_build_location}" | |
| 19 | 23 #end if |
| 16 | 24 #end if |
| 13 | 25 #if str($genome_resource_library.build_type) == "specify_built_location": |
| 26 --build_location="${genome_resource_library.built_library_location}" | |
| 0 | 27 #end if |
| 15 | 28 #if str($gmap_options.gmap_build) == "true": |
| 29 --gmap_build | |
| 30 #if str($gmap_options.force_gmap_build) == "true": | |
| 31 --force_gmap_build | |
| 32 #end if | |
| 33 #end if | |
| 14 | 34 #if str($mutation_lib_options.mutation_build) == "true": |
| 35 --download_mutation_resources_url="${mutation_lib_options.source_url}" | |
| 36 --cosmic_resources_location="${mutation_lib_options.cosmic_files_location}" | |
| 37 #if str($mutation_lib_options.force_download) == "true": | |
| 38 --new_mutation_download | |
| 39 #end if | |
| 40 #if str($mutation_lib_options.redo_integration) == "true": | |
| 41 --new_mutation_integration | |
| 42 #end if | |
| 43 #end if | |
| 0 | 44 ]]> |
| 45 </command> | |
| 46 <inputs> | |
| 47 <!-- The following are left in here, just as examples of various ways of doing options. | |
| 48 <param name="force_download" type="boolean" checked="false" | |
| 49 truevalue="- -force_download" falsevalue="" label="Force New Download? (yes/no)" /> | |
| 50 <param name="download" type="select" label="Need to Download?"> | |
| 51 <option value="single" selected="true">Single Dataset</option> | |
| 52 <option value="paired_collection">Paired Collection</option> | |
| 53 <when value="paired_collection"> | |
| 54 <param name="fastq_input" format="fastqsanger" type="data_collection" collection_type="paired" label="Select dataset pair" help="Specify paired dataset collection containing paired reads"/> | |
| 55 </when> | |
| 56 --> | |
| 8 | 57 <conditional name="genome_resource_library"> |
| 10 | 58 <param name="build_type" type="select" label="Download CTAT Genome Resource Library?"> |
| 59 <option value="download_and_build" selected="true">Download from CTAT and build if needed</option> | |
| 60 <option value="build_from_source">Build library from local source data</option> | |
| 61 <option value="specify_built_location">Specify location of built library</option> | |
| 0 | 62 </param> |
| 10 | 63 <when value="download_and_build"> |
| 0 | 64 <!-- The use of a code block to get dynamic options is now deprecated and discouraged. |
| 65 I am still using it here. The only other way I can think of to do this is to | |
| 66 create another data_manager that gets the list of files and puts them into a | |
| 67 data_table, that is then used to get the filenames. That would require the admin | |
| 68 to first run the data_manager that builds the filename data_table before running | |
| 69 this data_manager. | |
| 70 This is the dynamic way to get the options filled. | |
| 71 <param name="filename" type="select" label="Select File" display="radio" | |
| 72 dynamic_options="get_ctat_genome_filenames()" | |
| 73 help="Select a CTAT Genome Resource Library to Download." /> | |
| 74 Here is the static method for what is online in April 2017: | |
| 75 <param name="filename" type="select" label="Choose which library to download."> | |
| 76 <option value="https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/GRCh37_v19_CTAT_lib_Feb092018.plug-n-play.tar.gz"> | |
| 77 GRCh37_v19_CTAT_lib_Feb092018.plug-n-play.tar.gz | |
| 78 </option> | |
| 79 <option value="https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/ GRCh37_v19_CTAT_lib_Feb092018.source_data.tar.gz"> | |
| 80 GRCh37_v19_CTAT_lib_Feb092018.source_data.tar.gz | |
| 81 </option> | |
| 82 <option value="https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/ GRCh38_v27_CTAT_lib_Feb092018.plug-n-play.tar.gz"> | |
| 83 GRCh38_v27_CTAT_lib_Feb092018.plug-n-play.tar.gz | |
| 84 </option> | |
| 85 <option value="https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/ GRCh38_v27_CTAT_lib_Feb092018.source_data.tar.gz"> | |
| 86 GRCh38_v27_CTAT_lib_Feb092018.source_data.tar.gz | |
| 87 </option> | |
| 88 <option value="https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/ Mouse_M16_CTAT_lib_Feb202018.plug-n-play.tar.gz"> | |
| 89 Mouse_M16_CTAT_lib_Feb202018.plug-n-play.tar.gz | |
| 90 </option> | |
| 91 <option value="https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/ Mouse_M16_CTAT_lib_Feb202018.source_data.tar.gz"> | |
| 92 Mouse_M16_CTAT_lib_Feb202018.source_data.tar.gz | |
| 93 </option> | |
| 94 --> | |
| 10 | 95 <param name="download_url" type="select" label="Select a File" |
| 0 | 96 dynamic_options="get_ctat_genome_urls()" |
| 1 | 97 help="Select a CTAT Genome Resource Library to Download."> |
| 0 | 98 </param> |
| 10 | 99 <param name="download_destination" type="text" label="Download Destination (full path)" /> |
| 100 <param name="force_new_download" type="boolean" checked="false" label="Force New Download?" /> | |
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101 <param name="keep_archive" type="boolean" checked="true" label="Keep downloaded archive rather than deleting after build?" /> |
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102 <param name="rebuild" type="boolean" checked="false" label="Force new build of Library?" /> |
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103 <conditional name="specify_build_location"> |
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104 <param name="build_location" type="select" label="Location of Built Library"> |
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105 <option value="same_as_download" selected="true">Build in Download location</option> |
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106 <option value="different_location">Build in a different location</option> |
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107 </param> |
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108 <when value="different_location"> |
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109 <param name="different_build_location" type="text" label="Build Location (full path)" /> |
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110 </when> |
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111 </conditional> |
| 10 | 112 </when> |
| 113 <when value="build_from_source"> | |
| 114 <param name="source_location" type="text" label="Location of Source Files (full path)" /> | |
| 115 <param name="rebuild" type="boolean" checked="false" label="Force new build of Library?" /> | |
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116 <conditional name="specify_build_location"> |
| 19 | 117 <param name="build_location" type="boolean" checked="false" label="Is the build location different than the source location?" /> |
| 118 <when value="true"> | |
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119 <param name="different_build_location" type="text" label="Build Location (full path)" /> |
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120 </when> |
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121 </conditional> |
| 10 | 122 </when> |
| 123 <when value="specify_built_location"> | |
| 124 <param name="built_library_location" type="text" label="Location of the Built Library (full path)" /> | |
| 0 | 125 </when> |
| 126 </conditional> | |
| 127 <param name="display_name" type="text" label="Reference Genome Display Name" /> | |
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128 <conditional name="gmap_options"> |
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129 <param name="gmap_build" type="boolean" checked="true" label="Do a gmap_build on the Library?" /> |
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130 <when value="true"> |
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131 <param name="force_gmap_build" type="boolean" checked="false" label="Force a new build even if previously done?" /> |
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132 </when> |
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133 </conditional> |
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134 <conditional name="mutation_lib_options"> |
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135 <param name="mutation_build" type="boolean" checked="false" label="Download mutation library?"> |
| 8 | 136 </param> |
| 137 <when value="true"> | |
| 138 <param name="source_url" type="select" label="Select a File" | |
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139 dynamic_options="get_mutation_lib_urls()" |
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140 help="Select CTAT Mutation Library File to Download.\nMake sure it is the right one for your CTAT Genome Resource Library!"> |
| 8 | 141 </param> |
| 142 <param name="force_download" type="boolean" checked="false" label="Force New Download?" /> | |
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143 <param name="redo_integration" type="boolean" checked="false" label="Redo Library Integration?" /> |
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144 <param name="cosmic_files_location" type="text" label="Location of the COSMIC files (See Tool Notes)." /> |
| 8 | 145 </when> |
| 146 </conditional> | |
| 10 | 147 --> |
| 0 | 148 </inputs> |
| 149 <outputs> | |
| 150 <data name="out_file" format="data_manager_json" /> | |
| 151 </outputs> | |
| 152 <help> | |
| 153 Retrieve, and/or specify the location of, a CTAT Genome Resource Library. | |
| 154 When download is true, the files at https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/ | |
| 155 are used as selectors for the user to choose among. | |
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156 Specify the Full Path of the location where the CTAT Genome Resource Library should be placed. |
| 3 | 157 You will need approximately 62GB of space for this library. |
| 158 The installation of this tool takes some time, due to building a conda environment for the dependencies. | |
| 159 The download extracts the files during the download. The "source_data" files download faster, but then must be built. | |
| 160 Building the library from the "source_data" files can take many hours, depending on the resources of your machine. | |
| 161 The "plug-n-play" can take considerable time to download, depending on your internet connection. Even with high speed, | |
| 162 it is about 25GB that is transfered, so plan accordingly. | |
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163 If you have a good speed internet connection, downloading the plug-n-play will usually be faster than building. |
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164 If a download or the build is interupted, re-running the job should pick up where it left off. |
| 3 | 165 Neither the "source_data" nor the "plug-n-play" versions have had their gmap index built. If you are not going to be |
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166 using gmap_fusion, then you can uncheck the gmap_build check box and save the space and time building the index consumes. |
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167 Neither the "source_data" nor the "plug-n-play" versions have mutation resources included. Those must be downloaded |
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168 separately. By default the Mutation Resources are not integrated into the Library. If you are going to be using the |
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169 ctat_mutations tool, check the Download Mutation Library check box. |
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170 In order to integrate the Mutation Resources into a CTAT Genome Resource Library, you must have previously downloaded |
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171 COSMIC resources (See Step 2 from |
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172 <a href="https://github.com/NCIP/ctat-mutations/tree/master/mutation_lib_prep">Mutation Lib Prep Information</a>.) |
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173 You can place them directly into the Genome Resource Library location, or if the Library is |
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174 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 |
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175 integrated into the Library. The Mouse genome is not currently supported in ctat_mutations. |
| 8 | 176 If you already have a CTAT Genome Resource library installed on your system, |
| 177 specify the full path of the location where it exists and leave the download box unchecked. | |
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178 The Reference Genome name may be left empty if downloading. |
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179 The filename will then be used as the selector text of the entry in the data table. |
| 8 | 180 For more information on CTAT Genome Resource Libraries, |
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181 see <a href="https://github.com/FusionFilter/FusionFilter/wiki">FusionFilter</a> |
| 0 | 182 </help> |
| 183 <code file="add_ctat_resource_lib.py" /> | |
| 184 </tool> |