Mercurial > repos > florianbegusch > qiime2_all
comparison qiime_feature-classifier_fit-classifier-sklearn.xml @ 0:09b7bcb72fa7 draft
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| author | florianbegusch |
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| date | Thu, 24 May 2018 02:11:44 -0400 |
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| -1:000000000000 | 0:09b7bcb72fa7 |
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| 1 <?xml version="1.0" ?> | |
| 2 <tool id="qiime_feature-classifier_fit-classifier-sklearn" name="qiime feature-classifier fit-classifier-sklearn" version="2018.4"> | |
| 3 <description>- Train an almost arbitrary scikit-learn classifier</description> | |
| 4 <requirements> | |
| 5 <requirement type="package" version="2018.4">qiime2</requirement> | |
| 6 </requirements> | |
| 7 <command> | |
| 8 <![CDATA[ | |
| 9 qiime feature-classifier fit-classifier-sklearn --p-classifier-specification="$pclassifierspecification" | |
| 10 | |
| 11 #if str( $id_to_taxonomy_fp.selector ) == 'history' | |
| 12 #set $tax = $id_to_taxonomy_fp.taxonomy_fp | |
| 13 --i-reference-taxonomy '$tax' | |
| 14 #else: | |
| 15 #set $tax = $id_to_taxonomy_fp.taxonomy_fp.fields.path | |
| 16 --i-reference-taxonomy '$tax' | |
| 17 #end if | |
| 18 | |
| 19 --i-reference-reads=$ireferencereads | |
| 20 #if str($iclassweight) != 'None': | |
| 21 --i-class-weight=$iclassweight | |
| 22 #end if | |
| 23 --o-classifier=oclassifier | |
| 24 #if str($cmdconfig) != 'None': | |
| 25 --cmd-config=$cmdconfig | |
| 26 #end if | |
| 27 ; | |
| 28 cp oclassifier.qza $oclassifier; | |
| 29 ]]> | |
| 30 </command> | |
| 31 <inputs> | |
| 32 <param format="qza,no_unzip.zip" label="--i-reference-reads: FeatureData[Sequence] [required]" name="ireferencereads" optional="False" type="data"/> | |
| 33 | |
| 34 <conditional name="id_to_taxonomy_fp" optional="True"> | |
| 35 <param name="selector" type="select" label="Reference taxonomy to query"> | |
| 36 <option value="cached">Public databases</option> | |
| 37 <option value="history">Databases from your history</option> | |
| 38 </param> | |
| 39 <when value="cached"> | |
| 40 <param argument="--taxonomy_fp" label="Reference taxonomy" type="select" optional="True"> | |
| 41 <options from_data_table="qiime_taxonomy" /> | |
| 42 </param> | |
| 43 </when> | |
| 44 <when value="history"> | |
| 45 <param argument="--taxonomy_fp" type="data" format="qza,no_unzip.zip" label="Reference databases" optional="True" /> | |
| 46 </when> | |
| 47 </conditional> | |
| 48 | |
| 49 <param format="qza,no_unzip.zip" label="--i-class-weight: FeatureTable[RelativeFrequency] [optional]" name="iclassweight" optional="True" type="data"/> | |
| 50 <param label="--p-classifier-specification: [required]" name="pclassifierspecification" optional="False" type="text"/> | |
| 51 <param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/> | |
| 52 </inputs> | |
| 53 <outputs> | |
| 54 <data format="qza" label="${tool.name} on ${on_string}: classifier.qza" name="oclassifier"/> | |
| 55 </outputs> | |
| 56 <help> | |
| 57 <![CDATA[ | |
| 58 Train an almost arbitrary scikit-learn classifier | |
| 59 ------------------------------------------------- | |
| 60 | |
| 61 Train a scikit-learn classifier to classify reads. | |
| 62 | |
| 63 Parameters | |
| 64 ---------- | |
| 65 reference_reads : FeatureData[Sequence] | |
| 66 \ | |
| 67 reference_taxonomy : FeatureData[Taxonomy] | |
| 68 \ | |
| 69 class_weight : FeatureTable[RelativeFrequency], optional | |
| 70 \ | |
| 71 classifier_specification : Str | |
| 72 \ | |
| 73 | |
| 74 Returns | |
| 75 ------- | |
| 76 classifier : TaxonomicClassifier | |
| 77 \ | |
| 78 ]]> | |
| 79 </help> | |
| 80 </tool> |