Mercurial > repos > dfornika > data_manager_build_kraken2_database
comparison data_manager/kraken2_build_custom.xml @ 4:988c436ad798 draft
planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_kraken2_database/ commit f05f93ee024df8b38efa1c92db9785d52c726f85-dirty
| author | dfornika |
|---|---|
| date | Fri, 01 Mar 2019 14:01:57 -0500 |
| parents | cf0cda80b659 |
| children | 1f6fe9dc5490 |
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| 3:b03007bc0f05 | 4:988c436ad798 |
|---|---|
| 5 <requirement type="package" version="2.0.7_beta">kraken2</requirement> | 5 <requirement type="package" version="2.0.7_beta">kraken2</requirement> |
| 6 </requirements> | 6 </requirements> |
| 7 <version_command>kraken2 -version | head -n 1 | awk '{print $NF}'</version_command> | 7 <version_command>kraken2 -version | head -n 1 | awk '{print $NF}'</version_command> |
| 8 <command detect_errors="exit_code"> | 8 <command detect_errors="exit_code"> |
| 9 <![CDATA[ | 9 <![CDATA[ |
| 10 python '$__tool_directory__/kraken2_build_standard.py' | 10 python '$__tool_directory__/kraken2_build_custom.py' |
| 11 '${out_file}' | 11 '${out_file}' |
| 12 --threads \${GALAXY_SLOTS:-1} | 12 --threads \${GALAXY_SLOTS:-1} |
| 13 --fasta ${input_fasta} | |
| 14 --kmer-len ${kmer_len} | 13 --kmer-len ${kmer_len} |
| 15 --minimizer-len ${minimizer_len} | 14 --minimizer-len ${minimizer_len} |
| 16 --minimizer-spaces ${minimizer_spaces} | 15 --minimizer-spaces ${minimizer_spaces} |
| 16 --fasta ${input_fasta} | |
| 17 ]]> | 17 ]]> |
| 18 </command> | 18 </command> |
| 19 <inputs> | 19 <inputs> |
| 20 <param name="input_fasta" type="data" format="fasta" multiple="False" optional="true" label="Select history item" /> | 20 <param name="input_fasta" type="data" format="fasta" multiple="False" optional="true" label="Select history item" /> |
| 21 <param name="kmer_len" type="integer" value="35" label="K-mer length in BP" /> | 21 <param name="kmer_len" type="integer" value="35" label="K-mer length in BP" /> |