Mercurial > repos > jjohnson > defuse

annotate datamanager_create_reference.xml @ 40:ed07bcc39f6e

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author Jim Johnson <jj@umn.edu>
date Wed, 06 May 2015 14:31:57 -0500
parents 68494d6aabeb
children 74de1ccc51db
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19
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1 <tool id="data_manager_defuse_reference" name="DeFuse Reference DataManager" version="1.6.1" tool_type="manage_data">
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2 <description>create a defuse reference from Ensembl and UCSC sources</description>
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3 <requirements>
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4 <requirement type="package" version="0.6.1">defuse</requirement>
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5 <requirement type="package" version="0.1.18">samtools</requirement>
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6 <requirement type="package" version="1.0.0">bowtie</requirement>
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7 <requirement type="package" version="2013-05-09">gmap</requirement>
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8 <requirement type="package" version="latest">kent</requirement>
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9 </requirements>
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10 <command interpreter="python"> datamanager_create_reference.py
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11 --dbkey $genome.ensembl_genome_version
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12 --description "$genome.ensembl_prefix $genome.ensembl_genome_version ($genome.ucsc_genome_version)"
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13 --defuse_config $defuse_config
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14 --defuse_script $defuse_script
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15 $out_file
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16 </command>
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17 <inputs>
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18 <conditional name="genome">
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19 <param name="choice" type="select" label="Select a Genome Build">
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20 <option value="GRCh37">Homo_sapiens GRCh37 hg19</option>
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21 <option value="NCBI36">Homo_sapiens NCBI36 hg18</option>
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22 <option value="GRCm38">Mus_musculus GRCm38 mm10</option>
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23 <option value="NCBIM37">Mus_musculus NCBIM37 mm9</option>
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24 <option value="Rnor_5.0">Rattus_norvegicus Rnor_5.0 rn5</option>
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25 <option value="user_specified">User specified</option>
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26 </param>
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27 <when value="GRCh37">
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28 <param name="ensembl_organism" type="hidden" value="homo_sapiens"/>
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29 <param name="ensembl_prefix" type="hidden" value="Homo_sapiens"/>
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30 <param name="ensembl_genome_version" type="hidden" value="GRCh37"/>
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31 <param name="ensembl_version" type="hidden" value="71"/>
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32 <param name="ncbi_organism" type="hidden" value="Homo_sapiens"/>
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33 <param name="ncbi_prefix" type="hidden" value="Hs"/>
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34 <param name="ucsc_genome_version" type="hidden" value="hg19"/>
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35 <param name="chromosomes" type="hidden" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,X,Y,MT"/>
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36 <param name="mt_chromosome" type="hidden" value="MT"/>
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37 <param name="gene_sources" type="hidden" value="IG_C_gene,IG_D_gene,IG_J_gene,IG_V_gene,processed_transcript,protein_coding"/>
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38 <param name="ig_gene_sources" type="hidden" value="IG_C_gene,IG_D_gene,IG_J_gene,IG_V_gene,IG_pseudogene"/>
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39 <param name="rrna_gene_sources" type="hidden" value="Mt_rRNA,rRNA,rRNA_pseudogene"/>
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40 </when>
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41 <when value="NCBI36">
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42 <param name="ensembl_organism" type="hidden" value="homo_sapiens"/>
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43 <param name="ensembl_prefix" type="hidden" value="Homo_sapiens"/>
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44 <param name="ensembl_genome_version" type="hidden" value="NCBI36"/>
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45 <param name="ensembl_version" type="hidden" value="54"/>
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46 <param name="ncbi_organism" type="hidden" value="Homo_sapiens"/>
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47 <param name="ncbi_prefix" type="hidden" value="Hs"/>
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48 <param name="ucsc_genome_version" type="hidden" value="hg18"/>
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49 <param name="chromosomes" type="hidden" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,X,Y,MT"/>
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50 <param name="mt_chromosome" type="hidden" value="MT"/>
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51 <param name="gene_sources" type="hidden" value="IG_C_gene,IG_D_gene,IG_J_gene,IG_V_gene,processed_transcript,protein_coding"/>
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52 <param name="ig_gene_sources" type="hidden" value="IG_C_gene,IG_D_gene,IG_J_gene,IG_V_gene,IG_pseudogene"/>
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53 <param name="rrna_gene_sources" type="hidden" value="Mt_rRNA,rRNA,rRNA_pseudogene"/>
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54 </when>
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55 <when value="GRCm38">
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56 <param name="ensembl_organism" type="hidden" value="mus_musculus"/>
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57 <param name="ensembl_prefix" type="hidden" value="Mus_musculus"/>
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58 <param name="ensembl_genome_version" type="hidden" value="GRCm38"/>
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59 <param name="ensembl_version" type="hidden" value="71"/>
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60 <param name="ncbi_organism" type="hidden" value="Mus_musculus"/>
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61 <param name="ncbi_prefix" type="hidden" value="Mm"/>
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62 <param name="ucsc_genome_version" type="hidden" value="mm10"/>
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63 <param name="chromosomes" type="hidden" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,X,Y,MT"/>
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64 <param name="mt_chromosome" type="hidden" value="MT"/>
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65 <param name="gene_sources" type="hidden" value="IG_C_gene,IG_D_gene,IG_J_gene,IG_V_gene,processed_transcript,protein_coding"/>
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66 <param name="ig_gene_sources" type="hidden" value="IG_C_gene,IG_D_gene,IG_J_gene,IG_V_gene,IG_pseudogene"/>
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67 <param name="rrna_gene_sources" type="hidden" value="Mt_rRNA,rRNA,rRNA_pseudogene"/>
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68 </when>
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69 <when value="NCBIM37">
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70 <param name="ensembl_organism" type="hidden" value="mus_musculus"/>
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71 <param name="ensembl_prefix" type="hidden" value="Mus_musculus"/>
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72 <param name="ensembl_genome_version" type="hidden" value="NCBIM37"/>
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73 <param name="ensembl_version" type="hidden" value="67"/>
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74 <param name="ncbi_organism" type="hidden" value="Mus_musculus"/>
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75 <param name="ncbi_prefix" type="hidden" value="Mm"/>
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76 <param name="ucsc_genome_version" type="hidden" value="mm9"/>
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77 <param name="chromosomes" type="hidden" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,X,Y,MT"/>
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78 <param name="mt_chromosome" type="hidden" value="MT"/>
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79 <param name="gene_sources" type="hidden" value="IG_C_gene,IG_D_gene,IG_J_gene,IG_V_gene,processed_transcript,protein_coding"/>
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80 <param name="ig_gene_sources" type="hidden" value="IG_C_gene,IG_D_gene,IG_J_gene,IG_V_gene,IG_pseudogene"/>
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81 <param name="rrna_gene_sources" type="hidden" value="Mt_rRNA,rRNA,rRNA_pseudogene"/>
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82 </when>
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83 <when value="Rnor_5.0">
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84 <param name="ensembl_organism" type="hidden" value="rattus_norvegicus"/>
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85 <param name="ensembl_prefix" type="hidden" value="Rattus_norvegicus"/>
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86 <param name="ensembl_genome_version" type="hidden" value="Rnor_5.0"/>
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87 <param name="ensembl_version" type="hidden" value="71"/>
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88 <param name="ncbi_organism" type="hidden" value="Rattus_norvegicus"/>
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89 <param name="ncbi_prefix" type="hidden" value="Rn"/>
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90 <param name="ucsc_genome_version" type="hidden" value="rn5"/>
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91 <param name="chromosomes" type="hidden" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,X,MT"/>
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92 <param name="mt_chromosome" type="hidden" value="MT"/>
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93 <param name="gene_sources" type="hidden" value="IG_C_gene,IG_D_gene,IG_J_gene,IG_V_gene,processed_transcript,protein_coding"/>
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94 <param name="ig_gene_sources" type="hidden" value="IG_C_gene,IG_D_gene,IG_J_gene,IG_V_gene,IG_pseudogene"/>
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95 <param name="rrna_gene_sources" type="hidden" value="Mt_rRNA,rRNA,rRNA_pseudogene"/>
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96 </when>
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97 <when value="user_specified">
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98 <param name="ensembl_organism" type="text" value="" label="Ensembl Organism Name" help="Examples: homo_sapiens, mus_musculus, rattus_norvegicus"/>
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99 <param name="ensembl_prefix" type="text" value="" label="Ensembl Organism prefix" help="Examples: Homo_sapiens, Mus_musculus, Rattus_norvegicus"/>
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100 <param name="ensembl_genome_version" type="text" value="" label="Ensembl Genome Version" help="Examples: GRCh37, GRCm38, Rnor_5.0"/>
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101 <param name="ensembl_version" type="integer" value="" label="Ensembl Release Version" help="Example: 71"/>
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102 <param name="ncbi_organism" type="text" value="" label="NCBI Organism Name" help="Examples: Homo_sapiens, Mus_musculus, Rattus_norvegicus"/>
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103 <param name="ncbi_prefix" type="text" value="" label="NCBI Organism Unigene prefix" help="Examples: Hs, Mm, Rn"/>
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104 <param name="ucsc_genome_version" type="text" value="" label="UCSC Genome Version" help="Examples: hg19, mm10, rn5"/>
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105 <param name="chromosomes" type="text" value="" label="Chromosomes for Ensembl genome build" >
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106 <help> Examples:
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107 Homo_sapiens: 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,X,Y,MT
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108 Mus_musculus: 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,X,Y,MT
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109 Rattus_norvegicus: 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,X,MT
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110 ( ftp://ftp.ensembl.org/pub/release-71/fasta/homo_sapiens/dna/ )
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111 </help>
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112 </param>
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113 <param name="mt_chromosome" type="text" value="MT" label="Ensembl Mitochonrial Chromosome name" />
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114 <param name="gene_sources" type="text" value="IG_C_gene,IG_D_gene,IG_J_gene,IG_V_gene,processed_transcript,protein_coding" label="Gene sources" />
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115 <param name="ig_gene_sources" type="text" value="IG_C_gene,IG_D_gene,IG_J_gene,IG_V_gene,IG_pseudogene" label="IG Gene sources" />
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116 <param name="rrna_gene_sources" type="text" value="Mt_rRNA,rRNA,rRNA_pseudogene" label="Ribosomal Gene sources" />
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117 </when>
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118 </conditional>
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119 </inputs>
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120 <outputs>
22
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121 <data name="out_file" format="data_manager_json" label="${tool.name} : ${genome.ensembl_genome_version}"/>
19
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122 </outputs>
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123 <stdio>
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124 <exit_code range="1:" level="fatal" description="Error running Create DeFuse Reference" />
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125 <regex match="Error:"
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126 source="both"
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127 level="fatal"
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128 description="Error running Create DeFuse Reference" />
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129
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130 </stdio>
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131 <configfiles>
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132 <configfile name="defuse_config">
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133 #
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134 # Configuration file for defuse
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135 #
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136 # Variables that desiganate the PATH to an application, e.g. __SAMTOOLS_BIN__
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137 # will be set by the runtime script using the ENV PATH
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138 #
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139
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140 # Directory where the defuse code was unpacked
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141 source_directory = __DEFUSE_PATH__
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142
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143 # Organism IDs
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144 ensembl_organism = $genome.ensembl_organism
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145 ensembl_prefix = $genome.ensembl_prefix
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146 ensembl_version = $genome.ensembl_version
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147 ensembl_genome_version = $genome.ensembl_genome_version
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148 ucsc_genome_version = $genome.ucsc_genome_version
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149 ncbi_organism = $genome.ncbi_organism
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150 ncbi_prefix = $genome.ncbi_prefix
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151
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152 # Directory where you want your dataset
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153 dataset_directory = __DATASET_DIRECTORY__
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154
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155 #raw
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156 # Input genome and gene models
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157 gene_models = $(dataset_directory)/$(ensembl_prefix).$(ensembl_genome_version).$(ensembl_version).gtf
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158 genome_fasta = $(dataset_directory)/$(ensembl_prefix).$(ensembl_genome_version).$(ensembl_version).dna.chromosomes.fa
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159
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160 # Repeat table from ucsc genome browser
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161 repeats_filename = $(dataset_directory)/repeats.txt
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162
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163 # EST info downloaded from ucsc genome browser
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164 est_fasta = $(dataset_directory)/est.fa
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165 est_alignments = $(dataset_directory)/intronEst.txt
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166
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167 # Unigene clusters downloaded from ncbi
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168 unigene_fasta = $(dataset_directory)/$(ncbi_prefix).seq.uniq
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169 #end raw
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170
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171 # Paths to external tools
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172 samtools_bin = __SAMTOOLS_BIN__
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173 bowtie_bin = __BOWTIE_BIN__
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174 bowtie_build_bin = __BOWTIE_BUILD_BIN__
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175 blat_bin = __BLAT_BIN__
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176 fatotwobit_bin = __FATOTWOBIT_BIN__
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177 gmap_bin = __GMAP_BIN__
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178 gmap_setup_bin = __GMAP_SETUP_BIN__
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179 r_bin = __R_BIN__
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180 rscript_bin = __RSCRIPT_BIN__
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181
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182 #raw
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183 # Directory where you want your dataset
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184 gmap_index_directory = $(dataset_directory)/gmap
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185 #end raw
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186
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187 #raw
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188 # Dataset files
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189 dataset_prefix = $(dataset_directory)/defuse
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190 chromosome_prefix = $(dataset_prefix).dna.chromosomes
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191 exons_fasta = $(dataset_prefix).exons.fa
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192 cds_fasta = $(dataset_prefix).cds.fa
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193 cdna_regions = $(dataset_prefix).cdna.regions
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194 cdna_fasta = $(dataset_prefix).cdna.fa
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195 reference_fasta = $(dataset_prefix).reference.fa
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196 rrna_fasta = $(dataset_prefix).rrna.fa
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197 ig_gene_list = $(dataset_prefix).ig.gene.list
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198 repeats_regions = $(dataset_directory)/repeats.regions
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199 est_split_fasta1 = $(dataset_directory)/est.1.fa
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200 est_split_fasta2 = $(dataset_directory)/est.2.fa
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201 est_split_fasta3 = $(dataset_directory)/est.3.fa
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202 est_split_fasta4 = $(dataset_directory)/est.4.fa
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203 est_split_fasta5 = $(dataset_directory)/est.5.fa
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204 est_split_fasta6 = $(dataset_directory)/est.6.fa
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205 est_split_fasta7 = $(dataset_directory)/est.7.fa
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206 est_split_fasta8 = $(dataset_directory)/est.8.fa
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207 est_split_fasta9 = $(dataset_directory)/est.9.fa
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208
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209 # Fasta files with bowtie indices for prefiltering reads for concordantly mapping pairs
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210 prefilter1 = $(unigene_fasta)
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211
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212 # deFuse scripts and tools
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213 scripts_directory = $(source_directory)/scripts
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214 tools_directory = $(source_directory)/tools
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215 data_directory = $(source_directory)/data
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216 #end raw
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217
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218 # Parameters for building the dataset
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219 chromosomes = $genome.chromosomes
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220 mt_chromosome = $genome.mt_chromosome
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221 gene_sources = $genome.gene_sources
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222 ig_gene_sources = $genome.ig_gene_sources
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223 rrna_gene_sources = $genome.rrna_gene_sources
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224
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225 #raw
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226 # Remove temp files
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227 remove_job_files = yes
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228 remove_job_temp_files = yes
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229 #end raw
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230 </configfile>
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231 <configfile name="defuse_script">
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232 #!/bin/bash
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233 ## define some things for cheetah proccessing
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234 #set $amp = chr(38)
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235 #set $gt = chr(62)
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236 ## substitute pathnames into config file
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237 if `grep __DATASET_DIRECTORY__ $defuse_config ${gt} /dev/null`;then sed -i'.tmp' "s#__DATASET_DIRECTORY__#\$1#" $defuse_config; fi
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238 if `grep __DEFUSE_PATH__ $defuse_config ${gt} /dev/null`;then sed -i'.tmp' "s#__DEFUSE_PATH__#\${DEFUSE_PATH}#" $defuse_config; fi
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239 if `grep __SAMTOOLS_BIN__ $defuse_config ${gt} /dev/null` ${amp}${amp} SAMTOOLS_BIN=`which samtools`;then sed -i'.tmp' "s#__SAMTOOLS_BIN__#\${SAMTOOLS_BIN}#" $defuse_config; fi
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240 if `grep __BOWTIE_BIN__ $defuse_config ${gt} /dev/null` ${amp}${amp} BOWTIE_BIN=`which bowtie`;then sed -i'.tmp' "s#__BOWTIE_BIN__#\${BOWTIE_BIN}#" $defuse_config; fi
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241 if `grep __BOWTIE_BUILD_BIN__ $defuse_config ${gt} /dev/null` ${amp}${amp} BOWTIE_BUILD_BIN=`which bowtie-build`;then sed -i'.tmp' "s#__BOWTIE_BUILD_BIN__#\${BOWTIE_BUILD_BIN}#" $defuse_config; fi
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242 if `grep __BLAT_BIN__ $defuse_config ${gt} /dev/null` ${amp}${amp} BLAT_BIN=`which blat`;then sed -i'.tmp' "s#__BLAT_BIN__#\${BLAT_BIN}#" $defuse_config; fi
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243 if `grep __FATOTWOBIT_BIN__ $defuse_config ${gt} /dev/null` ${amp}${amp} FATOTWOBIT_BIN=`which faToTwoBit`;then sed -i'.tmp' "s#__FATOTWOBIT_BIN__#\${FATOTWOBIT_BIN}#" $defuse_config; fi
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244 if `grep __GMAP_BIN__ $defuse_config ${gt} /dev/null` ${amp}${amp} GMAP_BIN=`which gmap`;then sed -i'.tmp' "s#__GMAP_BIN__#\${GMAP_BIN}#" $defuse_config; fi
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245 if `grep __GMAP_SETUP_BIN__ $defuse_config ${gt} /dev/null` ${amp}${amp} GMAP_SETUP_BIN=`which gmap_setup`;then sed -i'.tmp' "s#__GMAP_SETUP_BIN__#\${GMAP_SETUP_BIN}#" $defuse_config; fi
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246 if `grep __GMAP_INDEX_DIR__ $defuse_config ${gt} /dev/null` ${amp}${amp} GMAP_INDEX_DIR=`pwd`/gmap;then sed -i'.tmp' "s#__GMAP_INDEX_DIR__#\${GMAP_INDEX_DIR}#" $defuse_config; fi
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247 if `grep __R_BIN__ $defuse_config ${gt} /dev/null` ${amp}${amp} R_BIN=`which R`;then sed -i'.tmp' "s#__R_BIN__#\${R_BIN}#" $defuse_config; fi
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248 if `grep __RSCRIPT_BIN__ $defuse_config ${gt} /dev/null` ${amp}${amp} RSCRIPT_BIN=`which Rscript`;then sed -i'.tmp' "s#__RSCRIPT_BIN__#\${RSCRIPT_BIN}#" $defuse_config; fi
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249 ## copy config to output
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250 cp $defuse_config \$1/defuse_config.txt
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251 ## Run the create_reference_dataset.pl
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252 perl \${DEFUSE_PATH}/scripts/create_reference_dataset.pl -c $defuse_config
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253 </configfile>
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254 </configfiles>
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255
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256 <tests>
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257 </tests>
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258 <help>
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259 **DeFuse**
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260
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261 DeFuse_ is a software package for gene fusion discovery using RNA-Seq data. The software uses clusters of discordant paired end alignments to inform a split read alignment analysis for finding fusion boundaries. The software also employs a number of heuristic filters in an attempt to reduce the number of false positives and produces a fully annotated output for each predicted fusion. See the DeFuse_Version_0.6_ manual for details.
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262
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263 DeFuse uses a Reference Dataset to search for gene fusions. The Reference Dataset is generated from the following sources in DeFuse_Version_0.6_:
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264 - genome_fasta from Ensembl
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265 - gene_models from Ensembl
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266 - repeats_filename from UCSC RepeatMasker rmsk.txt
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267 - est_fasta from UCSC
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268 - est_alignments from UCSC intronEst.txt
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269 - unigene_fasta from NCBI
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270
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271 The create_defuse_reference Galaxy tool downloads the reference genome and other source files, and builds any derivative files including bowtie indices, gmap indices, and 2bit files. Expect this step to take at least 12 hours.
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272
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273
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274 It will generate the refernce data for deFuse Galaxy tool.
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275
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276 Journal reference: http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1001138
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277
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278 .. _DeFuse: http://sourceforge.net/apps/mediawiki/defuse/index.php?title=Main_Page
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279
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280 .. _DeFuse_Version_0.6: http://sourceforge.net/apps/mediawiki/defuse/index.php?title=DeFuse_Version_0.6.1
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281
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282 ------
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283
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284 **Outputs**
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285
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286 The galaxy history will contain: the config.txt file that provides DeFuse with the reference data paths.
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287
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288 </help>
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289 </tool>