Mercurial > repos > scottx611x > data_manager_fetch_gene_annotation
view data_manager_gene_annotation/data_manager/gene_annotation_fetcher.xml @ 43:e42284a13168 draft
planemo upload
author | scottx611x |
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date | Fri, 08 Jul 2016 14:45:18 -0400 |
parents | 87a921902f5e |
children |
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<?xml version="1.0"?> <tool id="gene_annotation_fetcher_data_manager" name="Gene Annotation Fetch" tool_type="manage_data" version="1.0.0"> <description>gene annotation fetcher</description> <stdio> <exit_code description="Error" level="fatal" range="1:" /> </stdio> <command interpreter="python"> <![CDATA[ data_manager.py --out "${out_file}" #if $gene_annotation_url: --url "${gene_annotation_url}" #end if #if $database_name: --name "${database_name}" #end if ]]> </command> <inputs> <param help="Enter a descriptive name to be used in the tool drop-down menus" label="Identifier for this DataTable entry" name="database_name" type="text" optional="True" /> <param label="Enter URL pointing to a remote GTF/GFF file" name="gene_annotation_url" type="text" optional="False"/> </inputs> <outputs> <data format="data_manager_json" name="out_file" /> </outputs> <tests> <test> <param name="database_name" value="cool_name"/> <param name="gene_annotation_url" value="http://www.scott-ouellette.com/gene_annotations/chr1-hg19_genes.gtf"/> <output name="out_file" file="gene_annotation_out.json" compare="contains"/> <!--<extra_files type="file" name="chr1-hg19_genes.gtf" value="chr1-hg19_genes.gtf"/>--> </test> </tests> </tool>