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