Mercurial > repos > estrain > data_manager_ganon

changeset 7:936dfddbcd74 draft

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Uploaded
author estrain
date Fri, 05 Jul 2019 08:50:48 -0400
parents 0ff53edee33d
children 63d5d3560e51
files data_manager/ganon_data_manager.xml
diffstat 1 files changed, 3 insertions(+), 6 deletions(-) [+]
line wrap: on
line diff
--- a/data_manager/ganon_data_manager.xml	Fri Jul 05 08:45:19 2019 -0400
+++ b/data_manager/ganon_data_manager.xml	Fri Jul 05 08:50:48 2019 -0400
@@ -1,14 +1,11 @@
 <tool id="ganon_data_manager" name="ganon data manager" version="0.0.1" tool_type="manage_data">
-    <description>Create ganon databases</description>
+    <description>Create entry for ganon databases</description>
     <requirements>
         <requirement type="package">ganon</requirement>
         <requirement type="package" version="3.7">python</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
-       python $__tool_directory__/fetch_ganon.py --rrna $rrna --output_directory $out_dir; 
-       python --version;
-       ganon build -d $rrna -i *.gz;
-       mv $rrna.* $out_dir;
+       python $__tool_directory__/add_table.py --rrna $rrna --output_directory $out_dir; 
     ]]></command>
     <inputs>
         <param argument="rrna" type="select" label="Bacterial rRNA loci">
@@ -22,7 +19,7 @@
         <data name="output_file" format="data_manager_json"/>
     </outputs>
     <help><![CDATA[
-    Retrieve RefSeq Bacterial rRNA Targeted Loci and build ganon database
+    Create entry for ganon databases in data table
     ]]>
     </help>
     <citations>