diff data_manager/fetch_vep_cache_data.xml @ 0:de3516853bde draft default tip

Uploaded
author davidvanzessen
date Fri, 30 Nov 2018 09:56:38 -0500
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/fetch_vep_cache_data.xml	Fri Nov 30 09:56:38 2018 -0500
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+<tool id="fetch_vep_cache_data" name="VEP Cache" version="0.0.1" tool_type="manage_data">
+  <requirements>
+    <requirement type="package" version="94.5">ensembl-vep</requirement>
+  </requirements>
+  <description>fetching</description>
+  
+  <command detect_errors="exit_code">
+python $__tool_directory__/fetch_vep_cache_data.py 
+--output-file ${ out_file } 
+--output-dir ${ out_file.extra_files_path } 
+--assembly ${ dbkey }${ extra }
+  </command>
+  <inputs>
+    <param name="dbkey" type="select" label="Species">
+      <option value="homo_sapiens">Human</option>
+      <option value="mus_musculus">Mouse</option>
+    </param>
+    <param name="extra" type="select" label="Get the Ensembl, Refseq or merged Ensembl/Refseq">
+      <option value="" selected="true">Ensembl</option>
+      <option value="_refseq">Refseq</option>
+      <option value="_merged">Merged</option>
+    </param>
+  </inputs>
+  <outputs>
+    <data name="out_file" format="data_manager_json"/>
+  </outputs>
+  <!-- 
+  <tests>
+      <test>
+          DON'T FORGET TO DEFINE SOME TOOL TESTS
+      </test>
+  </tests>
+  -->
+  <help>
+  There is no help
+  </help>
+</tool>
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