Mercurial > repos > florianbegusch > qiime2_suite
comparison qiime2/qiime_taxa_collapse.xml @ 0:370e0b6e9826 draft
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| author | florianbegusch |
|---|---|
| date | Wed, 17 Jul 2019 03:05:17 -0400 |
| parents | |
| children | de4c22a52df4 |
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| -1:000000000000 | 0:370e0b6e9826 |
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| 1 <?xml version="1.0" ?> | |
| 2 <tool id="qiime_taxa_collapse" name="qiime taxa collapse" version="2019.4"> | |
| 3 <description> - Collapse features by their taxonomy at the specified level</description> | |
| 4 <requirements> | |
| 5 <requirement type="package" version="2019.4">qiime2</requirement> | |
| 6 </requirements> | |
| 7 <command><![CDATA[ | |
| 8 qiime taxa collapse | |
| 9 | |
| 10 --i-table=$itable | |
| 11 --i-taxonomy=$itaxonomy | |
| 12 --p-level="$plevel" | |
| 13 | |
| 14 --o-collapsed-table=ocollapsedtable | |
| 15 ; | |
| 16 cp ocollapsedtable.qza $ocollapsedtable | |
| 17 ]]></command> | |
| 18 <inputs> | |
| 19 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] Feature table to be collapsed. [required]" name="itable" optional="False" type="data"/> | |
| 20 <param format="qza,no_unzip.zip" label="--i-taxonomy: ARTIFACT FeatureData[Taxonomy] Taxonomic annotations for features in the provided feature table. All features in the feature table must have a corresponding taxonomic annotation. Taxonomic annotations that are not present in the feature table will be ignored. [required]" name="itaxonomy" optional="False" type="data"/> | |
| 21 <param label="--p-level: INTEGER The taxonomic level at which the features should be collapsed. All ouput features will have exactly this many levels of taxonomic annotation. [required]" name="plevel" optional="False" value="" type="integer"/> | |
| 22 </inputs> | |
| 23 <outputs> | |
| 24 <data format="qza" label="${tool.name} on ${on_string}: collapsedtable.qza" name="ocollapsedtable"/> | |
| 25 </outputs> | |
| 26 <help><![CDATA[ | |
| 27 Collapse features by their taxonomy at the specified level | |
| 28 ########################################################## | |
| 29 | |
| 30 Collapse groups of features that have the same taxonomic assignment through | |
| 31 the specified level. The frequencies of all features will be summed when | |
| 32 they are collapsed. | |
| 33 | |
| 34 Parameters | |
| 35 ---------- | |
| 36 table : FeatureTable[Frequency] | |
| 37 Feature table to be collapsed. | |
| 38 taxonomy : FeatureData[Taxonomy] | |
| 39 Taxonomic annotations for features in the provided feature table. All | |
| 40 features in the feature table must have a corresponding taxonomic | |
| 41 annotation. Taxonomic annotations that are not present in the feature | |
| 42 table will be ignored. | |
| 43 level : Int | |
| 44 The taxonomic level at which the features should be collapsed. All | |
| 45 ouput features will have exactly this many levels of taxonomic | |
| 46 annotation. | |
| 47 | |
| 48 Returns | |
| 49 ------- | |
| 50 collapsed_table : FeatureTable[Frequency] | |
| 51 The resulting feature table, where all features are now taxonomic | |
| 52 annotations with the user-specified number of levels. | |
| 53 ]]></help> | |
| 54 <macros> | |
| 55 <import>qiime_citation.xml</import> | |
| 56 </macros> | |
| 57 <expand macro="qiime_citation"/> | |
| 58 </tool> |