Mercurial > repos > iuc > bracken
comparison est-abundance.xml @ 0:b7b1c8bf7ae0 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
| author | iuc |
|---|---|
| date | Wed, 16 Oct 2019 16:57:55 -0400 |
| parents | |
| children | a5145865e467 |
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| -1:000000000000 | 0:b7b1c8bf7ae0 |
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| 1 <tool id="est_abundance" name="Estimate Abundance at Taxonomic Level" version="@VERSION@+galaxy0"> | |
| 2 <description>Bayesian Reestimation of Abundance with KrakEN</description> | |
| 3 <macros> | |
| 4 <import>macros.xml</import> | |
| 5 </macros> | |
| 6 <edam_topics> | |
| 7 <edam_topic>topic_3174</edam_topic> | |
| 8 <edam_topic>topic_3697</edam_topic> | |
| 9 </edam_topics> | |
| 10 <edam_operations> | |
| 11 <edam_operation>operation_2238</edam_operation> | |
| 12 </edam_operations> | |
| 13 <expand macro="requirements" /> | |
| 14 <command detect_errors="exit_code"><![CDATA[ | |
| 15 est_abundance.py | |
| 16 -i '$input' | |
| 17 -k '$kmer_distr.fields.path' | |
| 18 -l $level | |
| 19 -t $threshold | |
| 20 -o '$report' | |
| 21 ]]> | |
| 22 </command> | |
| 23 <inputs> | |
| 24 <param name="input" type="data" format="tabular" label="Kraken report file" /> | |
| 25 <param label="Select a Kmer distribution" name="kmer_distr" type="select"> | |
| 26 <options from_data_table="bracken_databases"> | |
| 27 <validator message="No database is available" type="no_options" /> | |
| 28 </options> | |
| 29 </param> | |
| 30 <param name="level" type="select" label="Level" help="Level to push all reads to" > | |
| 31 <option value="S" selected="true">Species</option> | |
| 32 <option value="G">Genus</option> | |
| 33 <option value="F">Family</option> | |
| 34 <option value="O">Order</option> | |
| 35 <option value="C">Class</option> | |
| 36 <option value="P">Phylum</option> | |
| 37 <option value="D">Domain</option> | |
| 38 </param> | |
| 39 <param name="threshold" type="integer" value="10" label="Number of mismatches allowed when matching tag" | |
| 40 help="Threshold for the minimum number of reads kraken must assign to a classification for that | |
| 41 classification to be considered in the final abundance estimation." /> | |
| 42 </inputs> | |
| 43 <outputs> | |
| 44 <data name="report" format="tabular" label="${tool.name} on ${on_string}: Report" /> | |
| 45 </outputs> | |
| 46 <tests> | |
| 47 <test> | |
| 48 <param name="input" value="NC_003198.1_simulated_kraken_report.txt" ftype="tabular"/> | |
| 49 <param name="level" value="S" /> | |
| 50 <param name="bracken_database" value="test_entry"/> | |
| 51 <output name="report" file="NC_003198.1_simulated_bracken_report.txt" ftype="tabular"/> | |
| 52 </test> | |
| 53 <test> | |
| 54 <param name="input" value="NC_011750.1_simulated_kraken_report.txt" ftype="tabular"/> | |
| 55 <param name="level" value="S" /> | |
| 56 <param name="bracken_database" value="test_entry"/> | |
| 57 <output name="report" file="NC_011750.1_simulated_bracken_report.txt" ftype="tabular"/> | |
| 58 </test> | |
| 59 </tests> | |
| 60 <help> | |
| 61 <![CDATA[ | |
| 62 Documentation can be found at `site <http://ccb.jhu.edu/software/bracken/index.shtml?t=manual>`_. | |
| 63 ]]></help> | |
| 64 <expand macro="citations" /> | |
| 65 </tool> |