Mercurial > repos > scottx611x > data_manager_fetch_gene_annotation
comparison 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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38:d27c122c2424 | 39:2ab076cf69df |
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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 $database_name: | |
14 --dbkey "${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> |