Mercurial > repos > florianbegusch > qiime2_wrappers
annotate qiime2/qiime_taxa_collapse.xml @ 4:71f124e02000 draft default tip
Fixes
| author | florianbegusch |
|---|---|
| date | Tue, 13 Aug 2019 07:40:25 -0400 (2019-08-13) |
| parents | 149432539226 |
| children |
| rev | line source |
|---|---|
| 2 | 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 | |
| 4 | 10 #if str( $id_to_taxonomy_fp.selector ) == 'history' |
| 11 #set $tax = $id_to_taxonomy_fp.taxonomy_fp | |
| 12 --i-taxonomy '$tax' | |
| 13 #else: | |
| 14 #set $tax = $id_to_taxonomy_fp.taxonomy_fp.fields.path | |
| 15 --i-taxonomy '$tax' | |
| 16 #end if | |
| 17 | |
| 18 | |
| 2 | 19 --i-table=$itable |
| 4 | 20 |
| 21 #if str($plevel): | |
| 22 --p-level="$plevel" | |
| 23 #end if | |
| 2 | 24 |
| 25 --o-collapsed-table=ocollapsedtable | |
| 26 ; | |
| 27 cp ocollapsedtable.qza $ocollapsedtable | |
| 28 ]]></command> | |
| 29 <inputs> | |
| 4 | 30 |
| 31 <conditional name="id_to_taxonomy_fp" optional="True"> | |
| 32 <param name="selector" type="select" label="Reference taxonomy to query"> | |
| 33 <option value="cached">Public databases</option> | |
| 34 <option value="history">Databases from your history</option> | |
| 35 </param> | |
| 36 <when value="cached"> | |
| 37 <param argument="--taxonomy_fp" label="Reference taxonomy" type="select" optional="True"> | |
| 38 <options from_data_table="qiime_taxonomy" /> | |
| 39 </param> | |
| 40 </when> | |
| 41 <when value="history"> | |
| 42 <param argument="--taxonomy_fp" type="data" format="qza,no_unzip.zip" label="Reference databases" optional="True" /> | |
| 43 </when> | |
| 44 </conditional> | |
| 45 | |
| 46 | |
| 2 | 47 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] Feature table to be collapsed. [required]" name="itable" optional="False" type="data"/> |
| 48 <param label="--p-level: INTEGER The taxonomic level at which the features should be collapsed. All ouput features will have exactly this many levels of taxonomic annotation. [required]" name="plevel" optional="False" value="" type="integer"/> | |
| 49 </inputs> | |
| 50 <outputs> | |
| 51 <data format="qza" label="${tool.name} on ${on_string}: collapsedtable.qza" name="ocollapsedtable"/> | |
| 52 </outputs> | |
| 53 <help><![CDATA[ | |
| 54 Collapse features by their taxonomy at the specified level | |
| 55 ########################################################## | |
| 56 | |
| 57 Collapse groups of features that have the same taxonomic assignment through | |
| 58 the specified level. The frequencies of all features will be summed when | |
| 59 they are collapsed. | |
| 60 | |
| 61 Parameters | |
| 62 ---------- | |
| 63 table : FeatureTable[Frequency] | |
| 64 Feature table to be collapsed. | |
| 65 taxonomy : FeatureData[Taxonomy] | |
| 66 Taxonomic annotations for features in the provided feature table. All | |
| 67 features in the feature table must have a corresponding taxonomic | |
| 68 annotation. Taxonomic annotations that are not present in the feature | |
| 69 table will be ignored. | |
| 70 level : Int | |
| 71 The taxonomic level at which the features should be collapsed. All | |
| 72 ouput features will have exactly this many levels of taxonomic | |
| 73 annotation. | |
| 74 | |
| 75 Returns | |
| 76 ------- | |
| 77 collapsed_table : FeatureTable[Frequency] | |
| 78 The resulting feature table, where all features are now taxonomic | |
| 79 annotations with the user-specified number of levels. | |
| 80 ]]></help> | |
| 81 <macros> | |
| 82 <import>qiime_citation.xml</import> | |
| 83 </macros> | |
| 84 <expand macro="qiime_citation"/> | |
| 85 </tool> |