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1 <tool id="ctat_genome_resource_libs_data_manager"
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2 name="CTAT Genome Resource Libraries Data Manager"
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3 version="2.0.0" tool_type="manage_data">
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4 <description>Retrieve, and/or specify the location of, a CTAT Genome Resource Library.
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5 </description>
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6 <requirements>
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7 <requirement type="package" version="2.7">python</requirement>
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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>
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10 </requirements>
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11 <command detect_errors="exit_code">
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12 <![CDATA[
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13 python $__tool_directory__/add_ctat_resource_lib.py
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14 --output_filename="${out_file}"
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15 --display_name="${display_name}"
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16 #if str( $genome_resource_library.build_type ) == "download_and_build":
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17 --download_url="${genome_resource_library.download_url}"
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18 --download_location="${genome_resource_library.download_destination}"
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19 #if str( $genome_resource_library.force_new_download ) == "true":
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20 --new_archive_download
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21 #end if
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22 #if str( $genome_resource_library.keep_archive ) == "true":
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23 --keep_archive
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24 #end if
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25 #if str( $genome_resource_library.rebuild ) == "true":
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26 --new_library_build
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27 #end if
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28 #if str( $genome_resource_library.specify_build_location.build_location ) == "true":
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29 --build_location="${genome_resource_library.specify_build_location.different_build_location}"
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30 #end if
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31 #elif str( $genome_resource_library.build_type ) == "build_from_source":
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32 --source_location "${genome_resource_library.source_location}"
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33 #if str( $genome_resource_library.rebuild ) == "true":
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34 --new_library_build
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35 #end if
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36 #if str( $genome_resource_library.specify_build_location.build_location ) == "true":
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37 --build_location="${genome_resource_library.specify_build_location.different_build_location}"
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38 #end if
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39 #elif str( $genome_resource_library.build_type ) == "specify_built_location":
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40 --build_location="${genome_resource_library.built_library_location}"
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41 #end if
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42
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43 #if str( $gmap_options.gmap_build ) == "true":
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44 --gmap_build
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45 #if str( $gmap_options.force_gmap_build ) == "true":
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46 --force_gmap_build
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47 #end if
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48 #end if
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49
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50 #if str( $mutation_lib_options.mutation_build ) == "true":
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51 --download_mutation_resources_url="${mutation_lib_options.source_url}"
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52 --cosmic_resources_location="${mutation_lib_options.cosmic_files_location}"
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53 #if str( $mutation_lib_options.force_download ) == "true":
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54 --new_mutation_download
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55 #end if
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56 #if str( $mutation_lib_options.redo_integration ) == "true":
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57 --new_mutation_integration
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58 #end if
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59 #end if
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60 ]]>
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61 </command>
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62 <inputs>
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63 <!-- The following are left in here, just as examples of various ways of doing options.
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64 <param name="force_download" type="boolean" checked="false"
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65 truevalue="- -force_download" falsevalue="" label="Force New Download? (yes/no)" />
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66 <param name="download" type="select" label="Need to Download?">
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67 <option value="single" selected="true">Single Dataset</option>
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68 <option value="paired_collection">Paired Collection</option>
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69 <when value="paired_collection">
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70 <param name="fastq_input" format="fastqsanger" type="data_collection" collection_type="paired" label="Select dataset pair" help="Specify paired dataset collection containing paired reads"/>
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71 </when>
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72 -->
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73 <conditional name="genome_resource_library">
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74 <param name="build_type" type="select" label="Download CTAT Genome Resource Library?">
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75 <option value="download_and_build" selected="true">Download from CTAT and build if needed</option>
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76 <option value="build_from_source">Build library from local source data</option>
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77 <option value="specify_built_location">Specify location of built library</option>
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78 </param>
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79 <when value="download_and_build">
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80 <!-- The use of a code block to get dynamic options is now deprecated and discouraged.
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81 I am still using it here. The only other way I can think of to do this is to
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82 create another data_manager that gets the list of files and puts them into a
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83 data_table, that is then used to get the filenames. That would require the admin
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84 to first run the data_manager that builds the filename data_table before running
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85 this data_manager.
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86 This is the dynamic way to get the options filled.
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87 <param name="filename" type="select" label="Select File" display="radio"
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88 dynamic_options="get_ctat_genome_filenames()"
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89 help="Select a CTAT Genome Resource Library to Download." />
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90 Here is the static method for what is online in April 2017:
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91 <param name="filename" type="select" label="Choose which library to download.">
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92 <option value="https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/GRCh37_v19_CTAT_lib_Feb092018.plug-n-play.tar.gz">
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93 GRCh37_v19_CTAT_lib_Feb092018.plug-n-play.tar.gz
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94 </option>
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95 <option value="https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/ GRCh37_v19_CTAT_lib_Feb092018.source_data.tar.gz">
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96 GRCh37_v19_CTAT_lib_Feb092018.source_data.tar.gz
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97 </option>
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98 <option value="https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/ GRCh38_v27_CTAT_lib_Feb092018.plug-n-play.tar.gz">
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99 GRCh38_v27_CTAT_lib_Feb092018.plug-n-play.tar.gz
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100 </option>
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101 <option value="https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/ GRCh38_v27_CTAT_lib_Feb092018.source_data.tar.gz">
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102 GRCh38_v27_CTAT_lib_Feb092018.source_data.tar.gz
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103 </option>
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104 <option value="https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/ Mouse_M16_CTAT_lib_Feb202018.plug-n-play.tar.gz">
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105 Mouse_M16_CTAT_lib_Feb202018.plug-n-play.tar.gz
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106 </option>
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107 <option value="https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/ Mouse_M16_CTAT_lib_Feb202018.source_data.tar.gz">
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108 Mouse_M16_CTAT_lib_Feb202018.source_data.tar.gz
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109 </option>
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110 -->
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111 <param name="download_url" type="select" label="Select a File"
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112 dynamic_options="get_ctat_genome_urls()"
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113 help="Select a CTAT Genome Resource Library to Download.">
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114 </param>
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115 <param name="download_destination" type="text" label="Download Destination (full path)" />
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116 <param name="force_new_download" type="boolean" checked="false" label="Force New Download?" />
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117 <param name="keep_archive" type="boolean" checked="true" label="Keep downloaded archive rather than deleting after build?" />
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118 <param name="rebuild" type="boolean" checked="false" label="Force new build of Library?" />
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119 <conditional name="specify_build_location">
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120 <param name="build_location" type="boolean" checked="false" label="Is the build location different than the source location?" />
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121 <when value="true">
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122 <param name="different_build_location" type="text" label="Build Location (full path)" />
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123 </when>
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124 </conditional>
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125 </when>
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126 <when value="build_from_source">
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127 <param name="source_location" type="text" label="Location of Source Files (full path)" />
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128 <param name="rebuild" type="boolean" checked="false" label="Force new build of Library?" />
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129 <conditional name="specify_build_location">
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130 <param name="build_location" type="boolean" checked="false" label="Is the build location different than the source location?" />
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131 <when value="true">
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132 <param name="different_build_location" type="text" label="Build Location (full path)" />
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133 </when>
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134 </conditional>
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135 </when>
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136 <when value="specify_built_location">
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137 <param name="built_library_location" type="text" label="Location of the Built Library (full path)" />
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138 </when>
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139 </conditional>
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140 <param name="display_name" type="text" label="Reference Genome Display Name" />
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141 <conditional name="gmap_options">
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142 <param name="gmap_build" type="boolean" checked="true" label="Do a gmap_build on the Library?" />
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143 <when value="true">
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144 <param name="force_gmap_build" type="boolean" checked="false" label="Force a new build even if previously done?" />
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145 </when>
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146 </conditional>
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147 <conditional name="mutation_lib_options">
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148 <param name="mutation_build" type="boolean" checked="false" label="Download and integrate mutation library?">
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149 </param>
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150 <when value="true">
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151 <param name="source_url" type="select" label="Select a File"
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152 dynamic_options="get_mutation_resource_urls()"
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153 help="Select CTAT Mutation Library File to Download.\nMake sure it is the right one for your CTAT Genome Resource Library!">
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154 </param>
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155 <param name="force_download" type="boolean" checked="false" label="Force New Download?" />
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156 <param name="redo_integration" type="boolean" checked="false" label="Redo Library Integration?" />
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157 <param name="cosmic_files_location" type="text" label="Location of the COSMIC files (See Tool Notes)." />
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158 </when>
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159 </conditional>
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160 -->
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161 </inputs>
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162 <outputs>
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163 <data name="out_file" format="data_manager_json" />
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164 </outputs>
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165 <help>
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166 Retrieve, and/or specify the location of, a CTAT Genome Resource Library.
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167
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168 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.
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169
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170 1) Download from CTAT and build if needed:
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171 This option uses the files at https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/
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172 as selectors for the user to choose among.
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173 Specify the Full Path of the location where the CTAT Genome Resource Library should be placed.
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174 The other options should be self-explanatory.
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175 2) Build library from local source data:
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176 This assumes that you have already downloaded the source data for a build and you want to build it.
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177 3) Specify location of built library:
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178 This assumes you already have a build library and need tell galaxy where it is.
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179
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180 All options allow the user to do a gmap_build on the library
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181 and also to integrate ctat-mutation resources into the library.
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182
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183 You will need approximately 62GB of space for this library, once it is built,
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184 but if downloading and building, to be safe provide at least 75GB.
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185
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186 The installation of this tool takes some time, due to building a conda environment for the dependencies.
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187 The "source_data" files download faster, but then must be built.
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188 Building the library from the "source_data" files can take many hours, depending on the resources of your machine.
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189 The "plug-n-play" can take considerable time to download, depending on your internet connection. Even with high speed,
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190 it is about 25GB that is transfered, so plan accordingly.
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191 If you have a good speed internet connection, downloading the plug-n-play will usually be faster than building.
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192
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193 **If a download or a build is interrupted, re-running the job should pick up where it left off.**
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194
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195 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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196 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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197
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198 Neither the "source_data" nor the "plug-n-play" versions have mutation resources included. Those must be downloaded
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199 separately. By default the Mutation Resources are not integrated into the Library. If you are going to be using the
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200 ctat_mutations tool, check the Download Mutation Library check box.
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201
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202 In order to integrate the Mutation Resources into a CTAT Genome Resource Library, you must have previously downloaded
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203 COSMIC resources (See Step 2 from https://github.com/NCIP/ctat-mutations/tree/master/mutation_lib_prep )
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204 You can place them directly into the Genome Resource Library location, or if the Library is
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205 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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206 integrated into the Library.
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207
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208 The Mouse genome is not currently supported by ctat_mutations.
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209
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210 If the Reference Genome Display Name is left empty a name will be created,
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211 but any text that will best guide the user can be entered here.
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212 It will be the text that is used for selecting the library in pull down lists
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213 requiring a Genome Reference Library resource (ctat_genome_resource_libs).
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214
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215 For more information on CTAT Genome Resource Libraries,
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216 see https://github.com/FusionFilter/FusionFilter/wiki
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217 </help>
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218 <code file="add_ctat_resource_lib.py" />
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219 </tool>
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