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comparison datamanager_create_reference.xml @ 41:74de1ccc51db

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Add GRCh38 hg38, minor fixes.
author Jim Johnson <jj@umn.edu>
date Fri, 18 Dec 2015 14:37:33 -0600
parents 68494d6aabeb
children aedaa66483f1
comparison
equal deleted inserted replaced
40:ed07bcc39f6e 41:74de1ccc51db
15 $out_file 15 $out_file
16 </command> 16 </command>
17 <inputs> 17 <inputs>
18 <conditional name="genome"> 18 <conditional name="genome">
19 <param name="choice" type="select" label="Select a Genome Build"> 19 <param name="choice" type="select" label="Select a Genome Build">
20 <option value="GRCh38">Homo_sapiens GRCh38 hg38</option>
20 <option value="GRCh37">Homo_sapiens GRCh37 hg19</option> 21 <option value="GRCh37">Homo_sapiens GRCh37 hg19</option>
21 <option value="NCBI36">Homo_sapiens NCBI36 hg18</option> 22 <option value="NCBI36">Homo_sapiens NCBI36 hg18</option>
22 <option value="GRCm38">Mus_musculus GRCm38 mm10</option> 23 <option value="GRCm38">Mus_musculus GRCm38 mm10</option>
23 <option value="NCBIM37">Mus_musculus NCBIM37 mm9</option> 24 <option value="NCBIM37">Mus_musculus NCBIM37 mm9</option>
24 <option value="Rnor_5.0">Rattus_norvegicus Rnor_5.0 rn5</option> 25 <option value="Rnor_5.0">Rattus_norvegicus Rnor_5.0 rn5</option>
25 <option value="user_specified">User specified</option> 26 <option value="user_specified">User specified</option>
26 </param> 27 </param>
28 <when value="GRCh38">
29 <param name="ensembl_organism" type="hidden" value="homo_sapiens"/>
30 <param name="ensembl_prefix" type="hidden" value="Homo_sapiens"/>
31 <param name="ensembl_genome_version" type="hidden" value="GRCh38"/>
32 <param name="ensembl_version" type="hidden" value="80"/>
33 <param name="ncbi_organism" type="hidden" value="Homo_sapiens"/>
34 <param name="ncbi_prefix" type="hidden" value="Hs"/>
35 <param name="ucsc_genome_version" type="hidden" value="hg38"/>
36 <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"/>
37 <param name="mt_chromosome" type="hidden" value="MT"/>
38 <param name="gene_sources" type="hidden" value="IG_C_gene,IG_D_gene,IG_J_gene,IG_V_gene,processed_transcript,protein_coding"/>
39 <param name="ig_gene_sources" type="hidden" value="IG_C_gene,IG_D_gene,IG_J_gene,IG_V_gene,IG_pseudogene"/>
40 <param name="rrna_gene_sources" type="hidden" value="Mt_rRNA,rRNA,rRNA_pseudogene"/>
41 </when>
27 <when value="GRCh37"> 42 <when value="GRCh37">
28 <param name="ensembl_organism" type="hidden" value="homo_sapiens"/> 43 <param name="ensembl_organism" type="hidden" value="homo_sapiens"/>
29 <param name="ensembl_prefix" type="hidden" value="Homo_sapiens"/> 44 <param name="ensembl_prefix" type="hidden" value="Homo_sapiens"/>
30 <param name="ensembl_genome_version" type="hidden" value="GRCh37"/> 45 <param name="ensembl_genome_version" type="hidden" value="GRCh37"/>
31 <param name="ensembl_version" type="hidden" value="71"/> 46 <param name="ensembl_version" type="hidden" value="71"/>
219 chromosomes = $genome.chromosomes 234 chromosomes = $genome.chromosomes
220 mt_chromosome = $genome.mt_chromosome 235 mt_chromosome = $genome.mt_chromosome
221 gene_sources = $genome.gene_sources 236 gene_sources = $genome.gene_sources
222 ig_gene_sources = $genome.ig_gene_sources 237 ig_gene_sources = $genome.ig_gene_sources
223 rrna_gene_sources = $genome.rrna_gene_sources 238 rrna_gene_sources = $genome.rrna_gene_sources
239 gene_biotypes = $genome.gene_sources
240 ig_gene_biotypes = $genome.ig_gene_sources
241 rrna_gene_biotypes = $genome.rrna_gene_sources
224 242
225 #raw 243 #raw
226 # Remove temp files 244 # Remove temp files
227 remove_job_files = yes 245 remove_job_files = yes
228 remove_job_temp_files = yes 246 remove_job_temp_files = yes
229 #end raw 247 #end raw
230 </configfile> 248 </configfile>
231 <configfile name="defuse_script"> 249 <configfile name="defuse_script">#slurp
232 #!/bin/bash 250 #!/bin/bash
233 ## define some things for cheetah proccessing 251 ## define some things for cheetah proccessing
234 #set $amp = chr(38) 252 #set $amp = chr(38)
235 #set $gt = chr(62) 253 #set $gt = chr(62)
236 ## substitute pathnames into config file 254 ## substitute pathnames into config file