Mercurial > repos > dfornika > chewbbaca_prepexternalschema
comparison chewbbaca_prepexternalschema.xml @ 2:6a7d52785b70 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 071e014d347109e5c18cc50595498d3d43ef0323-dirty"
| author | dfornika |
|---|---|
| date | Tue, 02 Jun 2020 23:35:22 +0000 |
| parents | eac851537d92 |
| children | 0f665cf63c02 |
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| 1:eac851537d92 | 2:6a7d52785b70 |
|---|---|
| 6 <command detect_errors="exit_code"><![CDATA[ | 6 <command detect_errors="exit_code"><![CDATA[ |
| 7 mkdir input_files && | 7 mkdir input_files && |
| 8 #for $f in in str( $input_fasta ).split(','): | 8 #for $f in in str( $input_fasta ).split(','): |
| 9 #set $filename = os.path.basename( str($f) ).replace(".dat", "") | 9 #set $filename = os.path.basename( str($f) ).replace(".dat", "") |
| 10 ln -s ${f} input_files/${filename}.fasta | 10 ln -s ${f} input_files/${filename}.fasta |
| 11 #end for | |
| 11 chewBBACA.py PrepExternalSchema | 12 chewBBACA.py PrepExternalSchema |
| 12 --cpu \${GALAXY_SLOTS:-1} | 13 --cpu \${GALAXY_SLOTS:-1} |
| 13 -i 'input_files' | 14 -i 'input_files' |
| 14 #if str( translation_table ) != "": | 15 #if str( translation_table ) != "": |
| 15 --tbl '${translation_table}' | 16 --tbl '${translation_table}' |