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comparison tool_dependencies.xml @ 2:de1b97beeca9 draft default tip

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planemo upload
author crs4
date Fri, 05 Aug 2016 06:01:44 -0400
parents 49622e048652
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1:49622e048652 2:de1b97beeca9
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool_dependency> 2 <tool_dependency>
3 <package name="kggseq" version="1.0_20160412"> 3 <package name="kggseq" version="1.0_20160707">
4 <install version="1.0"> 4 <install version="1.0">
5 <actions> 5 <actions>
6 <action type="download_by_url" target_filename="kggseq_archive-v1.0_20160412.tar.gz">https://github.com/crs4/kggseq_archive/archive/v1.0_20160412.tar.gz</action> 6 <action type="download_by_url" target_filename="kggseq_archive-v1.0_20160707.tar.gz">https://github.com/crs4/kggseq_archive/archive/v1.0_20160707.tar.gz</action>
7 <action type="shell_command">java -jar kggseq.jar --no-lib-check --resource resources --buildver hg19 --db-filter 1kgeur201305,1kgeas201305,1kgafr201305,1kgsas201305,1kgamr201305,1kg201305,1kg201204,1kgafr201204,1kgeur201204,1kgamr201204,1kgasn201204,dbsnp135,dbsnp137,dbsnp138,dbsnp138nf,dbsnp141,ESP6500AA,ESP6500EA,exac --genome-annot --db-gene refgene,gencode,knowngene,ensembl --db-score dbnsfp --superdup-annot --cosmic-annot --omim-annot --scsnv-annot --mouse-pheno --zebrafish-pheno --ddd-annot --mendel-causing-predict all --patho-gene-predict --dgv-cnv-annot --o-flanking-seq 10 --vcf-file examples-lite/rare.disease.hg19.vcf</action> 7 <action type="shell_command">java -jar kggseq.jar --no-lib-check --resource resources --buildver hg19 --db-filter 1kgeur201305,1kgeas201305,1kgafr201305,1kgsas201305,1kgamr201305,1kg201305,1kg201204,1kgafr201204,1kgeur201204,1kgamr201204,1kgasn201204,dbsnp135,dbsnp137,dbsnp138,dbsnp138nf,dbsnp141,ESP6500AA,ESP6500EA,exac --genome-annot --db-gene refgene,gencode,knowngene,ensembl --db-score dbnsfp --superdup-annot --cosmic-annot --omim-annot --scsnv-annot --mouse-pheno --zebrafish-pheno --ddd-annot --mendel-causing-predict all --patho-gene-predict --dgv-cnv-annot --o-flanking-seq 10 --vcf-file examples-lite/rare.disease.hg19.vcf</action>
8 <action type="move_directory_files"> 8 <action type="move_directory_files">
9 <source_directory>.</source_directory> 9 <source_directory>.</source_directory>
10 <destination_directory>$INSTALL_DIR</destination_directory> 10 <destination_directory>$INSTALL_DIR</destination_directory>
11 </action> 11 </action>