|
0
|
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>
|
|
22
|
19 <param help="Enter a unique identifier, or leave blank for an auto-generated uuid" label="Name for this database" name="database_name" type="text" optional="True" />
|
|
11
|
20 <param label="Enter URL for gene annotation files" name="gene_annotation_url" type="text" optional="False"/>
|
|
0
|
21 </inputs>
|
|
|
22 <outputs>
|
|
|
23 <data format="data_manager_json" name="out_file" />
|
|
|
24 </outputs>
|
|
22
|
25 <tests>
|
|
|
26 <test>
|
|
|
27 <param name="database_name" value="cool_name"/>
|
|
|
28 <param name="gene_annotation_url" value="http://www.scott-ouellette.com/gene_annotations/chr1-hg19_genes.gtf"/>
|
|
|
29 <output name="out_file" file="chr1-hg19_genes.gtf.data_manager_json"/>
|
|
|
30 </test>
|
|
|
31 </tests>
|
|
0
|
32 </tool>
|
