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comparison datamanager_create_reference.xml @ 16:bdd93719cede draft

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author jjohnson
date Mon, 18 Dec 2017 09:31:31 -0500
parents b67c24d902aa
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15:b67c24d902aa 16:bdd93719cede
1 <tool id="data_manager_defuse_reference" name="DeFuse Reference DataManager" version="1.6.1" tool_type="manage_data"> 1 <tool id="data_manager_defuse_reference" name="DeFuse Reference DataManager" version="@DEFUSE_VERSION@.2" tool_type="manage_data">
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 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <requirements> 6 <requirements>
110 <param name="rrna_gene_sources" type="hidden" value="Mt_rRNA,rRNA,rRNA_pseudogene"/> 110 <param name="rrna_gene_sources" type="hidden" value="Mt_rRNA,rRNA,rRNA_pseudogene"/>
111 </when> 111 </when>
112 <when value="user_specified"> 112 <when value="user_specified">
113 <param name="ensembl_organism" type="text" value="" label="Ensembl Organism Name" help="Examples: homo_sapiens, mus_musculus, rattus_norvegicus"/> 113 <param name="ensembl_organism" type="text" value="" label="Ensembl Organism Name" help="Examples: homo_sapiens, mus_musculus, rattus_norvegicus"/>
114 <param name="ensembl_prefix" type="text" value="" label="Ensembl Organism prefix" help="Examples: Homo_sapiens, Mus_musculus, Rattus_norvegicus"/> 114 <param name="ensembl_prefix" type="text" value="" label="Ensembl Organism prefix" help="Examples: Homo_sapiens, Mus_musculus, Rattus_norvegicus"/>
115 <param name="ensembl_genome_version" type="text" value="" label="Ensembl Genome Version" help="Examples: GRCh37, GRCm38, Rnor_5.0"/> 115 <param name="ensembl_genome_version" type="text" value="" label="Ensembl Genome Version" help="Examples: GRCh38, GRCh37, GRCm38, Rnor_5.0"/>
116 <param name="ensembl_version" type="integer" value="" label="Ensembl Release Version" help="Example: 71"/> 116 <param name="ensembl_version" type="integer" value="" label="Ensembl Release Version" help="Example: 86"/>
117 <param name="ncbi_organism" type="text" value="" label="NCBI Organism Name" help="Examples: Homo_sapiens, Mus_musculus, Rattus_norvegicus"/> 117 <param name="ncbi_organism" type="text" value="" label="NCBI Organism Name" help="Examples: Homo_sapiens, Mus_musculus, Rattus_norvegicus"/>
118 <param name="ncbi_prefix" type="text" value="" label="NCBI Organism Unigene prefix" help="Examples: Hs, Mm, Rn"/> 118 <param name="ncbi_prefix" type="text" value="" label="NCBI Organism Unigene prefix" help="Examples: Hs, Mm, Rn"/>
119 <param name="ucsc_genome_version" type="text" value="" label="UCSC Genome Version" help="Examples: hg19, mm10, rn5"/> 119 <param name="ucsc_genome_version" type="text" value="" label="UCSC Genome Version" help="Examples: hg38, hg19, mm10, rn5"/>
120 <param name="chromosomes" type="text" value="" label="Chromosomes for Ensembl genome build" > 120 <param name="chromosomes" type="text" value="" label="Chromosomes for Ensembl genome build" >
121 <help> Examples: 121 <help> Examples:
122 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 122 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
123 Mus_musculus: 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,X,Y,MT 123 Mus_musculus: 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,X,Y,MT
124 Rattus_norvegicus: 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,X,MT 124 Rattus_norvegicus: 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,X,MT