Mercurial > repos > scottx611x > data_manager_fetch_gene_annotation
comparison data_manager_gene_annotation/data_manager/gene_annotation_fetcher.xml @ 40:87a921902f5e draft
planemo upload
| author | scottx611x |
|---|---|
| date | Fri, 08 Jul 2016 11:32:41 -0400 |
| parents | |
| children | e42284a13168 |
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| 39:2ab076cf69df | 40:87a921902f5e |
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| 1 <?xml version="1.0"?> | |
| 2 <tool id="gene_annotation_fetcher_data_manager" name="Gene Annotation Fetch" tool_type="manage_data" version="1.0.0"> | |
| 3 <description>gene annotation fetcher</description> | |
| 4 <stdio> | |
| 5 <exit_code description="Error" level="fatal" range="1:" /> | |
| 6 </stdio> | |
| 7 <command interpreter="python"> | |
| 8 <![CDATA[ | |
| 9 data_manager.py --out "${out_file}" | |
| 10 #if $gene_annotation_url: | |
| 11 --url "${gene_annotation_url}" | |
| 12 #end if | |
| 13 #if $database_name: | |
| 14 --name "${database_name}" | |
| 15 #end if | |
| 16 ]]> | |
| 17 </command> | |
| 18 <inputs> | |
| 19 <param | |
| 20 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" /> | |
| 21 <param | |
| 22 label="Enter URL pointing to a remote .gtf file" name="gene_annotation_url" type="text" optional="False"/> | |
| 23 </inputs> | |
| 24 <outputs> | |
| 25 <data format="data_manager_json" name="out_file" /> | |
| 26 </outputs> | |
| 27 <tests> | |
| 28 <test> | |
| 29 <param name="database_name" value="cool_name"/> | |
| 30 <param name="gene_annotation_url" value="http://www.scott-ouellette.com/gene_annotations/chr1-hg19_genes.gtf"/> | |
| 31 <output name="out_file" file="gene_annotation_out.json" compare="contains"/> | |
| 32 <!--<extra_files type="file" name="chr1-hg19_genes.gtf" value="chr1-hg19_genes.gtf"/>--> | |
| 33 </test> | |
| 34 </tests> | |
| 35 </tool> |