Mercurial > repos > iuc > biom_summarize_table
comparison biom_summarize_table.xml @ 0:8f4407e9891c draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
| author | iuc |
|---|---|
| date | Wed, 11 Sep 2019 12:39:57 -0400 |
| parents | |
| children | 2cc55cbcb4a3 |
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| -1:000000000000 | 0:8f4407e9891c |
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| 1 <tool id="biom_summarize_table" name="Summarize sample or observation data" version="@VERSION@.1"> | |
| 2 <description>in a BIOM table</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"> | |
| 9 <![CDATA[ | |
| 10 biom summarize-table | |
| 11 --input-fp '$input_fp' | |
| 12 --output-fp '$output_fp' | |
| 13 $qualitative | |
| 14 $observations | |
| 15 ]]> | |
| 16 </command> | |
| 17 <inputs> | |
| 18 <param name="input_fp" argument="--input-fp" type="data" format="biom1" label="Input BIOM table" /> | |
| 19 <param argument="--qualitative" type="boolean" checked="True" truevalue="--qualitative" falsevalue="" label="Present counts as number of unique observation ids per sample, rather than counts of observations per sample" /> | |
| 20 <param argument="--observations" type="boolean" checked="True" truevalue="--observations" falsevalue="" label="Summarize over observations" /> | |
| 21 </inputs> | |
| 22 <outputs> | |
| 23 <data format="text" name="output_fp"/> | |
| 24 </outputs> | |
| 25 <tests> | |
| 26 <test> | |
| 27 <param name="input_fp" value="input_abundance_1.biom1" /> | |
| 28 <param name="qualitative" value="" /> | |
| 29 <param name="observations" value="" /> | |
| 30 <output name="output_fp" value="summarize" compare="sim_size"/> | |
| 31 </test> | |
| 32 <test> | |
| 33 <param name="input_fp" value="input_abundance_1.biom1" /> | |
| 34 <param name="qualitative" value="--qualitative" /> | |
| 35 <param name="observations" value="--observations" /> | |
| 36 <output name="output_fp" value="summarize_qualitative_observations" compare="sim_size"/> | |
| 37 </test> | |
| 38 </tests> | |
| 39 <help><![CDATA[ | |
| 40 Provides details on the observation counts per sample, including summary statistics, as well as metadata categories associated with samples and observations. | |
| 41 ]]></help> | |
| 42 <expand macro="citations" /> | |
| 43 </tool> |