Mercurial > repos > scottx611x > data_manager_fetch_gene_annotation
diff data_manager/gene_annotation_fetcher.xml @ 39:2ab076cf69df draft
planemo upload for repository https://scottx611x@toolshed.g2.bx.psu.edu/repos/scottx611x/data_manager_fetch_gene_annotation
author | scottx611x |
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date | Fri, 08 Jul 2016 11:17:50 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager/gene_annotation_fetcher.xml Fri Jul 08 11:17:50 2016 -0400 @@ -0,0 +1,35 @@ +<?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 $database_name: + --dbkey "${database_name}" + #end if + ]]> + </command> + <inputs> + <param + help="Enter a unique identifier for the Data Table column to be created, or leave blank for an auto-generated uuid" label="Identifier for this DataTable entry" name="database_name" type="text" optional="True" /> + <param + label="Enter URL pointing to a remote .gtf 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>