Mercurial > repos > jjohnson > contig_annotation_tool

diff cat_prepare.xml @ 0:ad7507073c3f draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
author jjohnson
date Sun, 24 Nov 2019 21:56:00 -0500
parents
children aaeb63501369
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cat_prepare.xml	Sun Nov 24 21:56:00 2019 -0500
@@ -0,0 +1,29 @@
+<tool id="cat_prepare" name="CAT prepare" version="@VERSION@.0">
+    <description>database for CAT - Contig Annotation Tool</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="version_command" />
+    <command detect_errors="exit_code"><![CDATA[
+        #import os.path
+        #set $catdb = $cat_db.files_path
+        mkdir -p $catdb &&
+        echo CAT_DB `date '+%Y-%m-%d'` "@DATABASE_FOLDER@" "@TAXONOMY_FOLDER@" > $cat_db &&
+        CAT prepare --fresh
+        --database_folder '$os.path.join($catdb,"@DATABASE_FOLDER@")'
+        --taxonomy_folder '$os.path.join($catdb,"@TAXONOMY_FOLDER@")'
+    ]]></command>
+    <inputs>
+    </inputs>
+    <outputs>
+        <data name="cat_db" format="cat_db" />
+    </outputs>
+    <help><![CDATA[
+**CAT prepare**
+Prepare CAT reference data for classifying metagomic contigs or genome assemblies.
+
+@COMMON_HELP@
+    ]]></help>
+    <expand macro="citations" />
+</tool>