Mercurial > repos > jjohnson > contig_annotation_tool
comparison cat_prepare.xml @ 0:ad7507073c3f draft
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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| -1:000000000000 | 0:ad7507073c3f |
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| 1 <tool id="cat_prepare" name="CAT prepare" version="@VERSION@.0"> | |
| 2 <description>database for CAT - Contig Annotation Tool</description> | |
| 3 <macros> | |
| 4 <import>macros.xml</import> | |
| 5 </macros> | |
| 6 <expand macro="requirements" /> | |
| 7 <expand macro="version_command" /> | |
| 8 <command detect_errors="exit_code"><![CDATA[ | |
| 9 #import os.path | |
| 10 #set $catdb = $cat_db.files_path | |
| 11 mkdir -p $catdb && | |
| 12 echo CAT_DB `date '+%Y-%m-%d'` "@DATABASE_FOLDER@" "@TAXONOMY_FOLDER@" > $cat_db && | |
| 13 CAT prepare --fresh | |
| 14 --database_folder '$os.path.join($catdb,"@DATABASE_FOLDER@")' | |
| 15 --taxonomy_folder '$os.path.join($catdb,"@TAXONOMY_FOLDER@")' | |
| 16 ]]></command> | |
| 17 <inputs> | |
| 18 </inputs> | |
| 19 <outputs> | |
| 20 <data name="cat_db" format="cat_db" /> | |
| 21 </outputs> | |
| 22 <help><![CDATA[ | |
| 23 **CAT prepare** | |
| 24 Prepare CAT reference data for classifying metagomic contigs or genome assemblies. | |
| 25 | |
| 26 @COMMON_HELP@ | |
| 27 ]]></help> | |
| 28 <expand macro="citations" /> | |
| 29 </tool> |