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comparison create_reference_dataset.xml @ 44:225750bf3770 draft

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author jjohnson
date Mon, 04 Jan 2016 15:55:00 -0500
parents a004033614d4
children aedaa66483f1
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40:ed07bcc39f6e 44:225750bf3770
1 <tool id="create_defuse_reference" name="Create DeFuse Reference" version="1.6.1"> 1 <tool id="create_defuse_reference" name="Create DeFuse Reference" version="@DEFUSE_VERSION@.1">
2 <description>create a defuse reference from Ensembl and UCSC sources</description> 2 <description>create a defuse reference from Ensembl and UCSC sources</description>
3 <requirements> 3 <macros>
4 <requirement type="package" version="0.6.1">defuse</requirement> 4 <import>macros.xml</import>
5 <requirement type="package" version="0.1.18">samtools</requirement> 5 </macros>
6 <requirement type="package" version="1.0.0">bowtie</requirement> 6 <requirements>
7 <requirement type="package" version="2013-05-09">gmap</requirement> 7 <expand macro="defuse_requirement" />
8 <requirement type="package" version="latest">kent</requirement> 8 <expand macro="mapping_requirements" />
9 </requirements> 9 </requirements>
10 <command interpreter="command"> /bin/bash $defuse_script </command> 10 <command interpreter="command"> /bin/bash $defuse_script </command>
11 <inputs> 11 <inputs>
12 <conditional name="genome"> 12 <conditional name="genome">
13 <param name="choice" type="select" label="Select a Genome Build"> 13 <param name="choice" type="select" label="Select a Genome Build">
14 <option value="GRCh38">Homo_sapiens GRCh38 hg38</option>
14 <option value="GRCh37">Homo_sapiens GRCh37 hg19</option> 15 <option value="GRCh37">Homo_sapiens GRCh37 hg19</option>
15 <option value="NCBI36">Homo_sapiens NCBI36 hg18</option> 16 <option value="NCBI36">Homo_sapiens NCBI36 hg18</option>
16 <option value="GRCm38">Mus_musculus GRCm38 mm10</option> 17 <option value="GRCm38">Mus_musculus GRCm38 mm10</option>
17 <option value="NCBIM37">Mus_musculus NCBIM37 mm9</option> 18 <option value="NCBIM37">Mus_musculus NCBIM37 mm9</option>
18 <option value="Rnor_5.0">Rattus_norvegicus Rnor_5.0 rn5</option> 19 <option value="Rnor_5.0">Rattus_norvegicus Rnor_5.0 rn5</option>
19 <option value="user_specified">User specified</option> 20 <option value="user_specified">User specified</option>
20 </param> 21 </param>
22 <when value="GRCh38">
23 <param name="ensembl_organism" type="hidden" value="homo_sapiens"/>
24 <param name="ensembl_prefix" type="hidden" value="Homo_sapiens"/>
25 <param name="ensembl_genome_version" type="hidden" value="GRCh38"/>
26 <param name="ensembl_version" type="hidden" value="80"/>
27 <param name="ncbi_organism" type="hidden" value="Homo_sapiens"/>
28 <param name="ncbi_prefix" type="hidden" value="Hs"/>
29 <param name="ucsc_genome_version" type="hidden" value="hg38"/>
30 <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"/>
31 <param name="mt_chromosome" type="hidden" value="MT"/>
32 <param name="gene_sources" type="hidden" value="IG_C_gene,IG_D_gene,IG_J_gene,IG_V_gene,processed_transcript,protein_coding"/>
33 <param name="ig_gene_sources" type="hidden" value="IG_C_gene,IG_D_gene,IG_J_gene,IG_V_gene,IG_pseudogene"/>
34 <param name="rrna_gene_sources" type="hidden" value="Mt_rRNA,rRNA,rRNA_pseudogene"/>
35 </when>
21 <when value="GRCh37"> 36 <when value="GRCh37">
22 <param name="ensembl_organism" type="hidden" value="homo_sapiens"/> 37 <param name="ensembl_organism" type="hidden" value="homo_sapiens"/>
23 <param name="ensembl_prefix" type="hidden" value="Homo_sapiens"/> 38 <param name="ensembl_prefix" type="hidden" value="Homo_sapiens"/>
24 <param name="ensembl_genome_version" type="hidden" value="GRCh37"/> 39 <param name="ensembl_genome_version" type="hidden" value="GRCh37"/>
25 <param name="ensembl_version" type="hidden" value="71"/> 40 <param name="ensembl_version" type="hidden" value="71"/>
218 chromosomes = $genome.chromosomes 233 chromosomes = $genome.chromosomes
219 mt_chromosome = $genome.mt_chromosome 234 mt_chromosome = $genome.mt_chromosome
220 gene_sources = $genome.gene_sources 235 gene_sources = $genome.gene_sources
221 ig_gene_sources = $genome.ig_gene_sources 236 ig_gene_sources = $genome.ig_gene_sources
222 rrna_gene_sources = $genome.rrna_gene_sources 237 rrna_gene_sources = $genome.rrna_gene_sources
238 gene_biotypes = $genome.gene_sources
239 ig_gene_biotypes = $genome.ig_gene_sources
240 rrna_gene_biotypes = $genome.rrna_gene_sources
223 241
224 #raw 242 #raw
225 # Remove temp files 243 # Remove temp files
226 remove_job_files = yes 244 remove_job_files = yes
227 remove_job_temp_files = yes 245 remove_job_temp_files = yes
284 **Outputs** 302 **Outputs**
285 303
286 The galaxy history will contain: the config.txt file that provides DeFuse with the reference data paths. 304 The galaxy history will contain: the config.txt file that provides DeFuse with the reference data paths.
287 305
288 </help> 306 </help>
307 <expand macro="citations"/>
289 </tool> 308 </tool>