Mercurial > repos > florianbegusch > qiime2_suite
diff qiime2/qiime_feature-classifier_fit-classifier-sklearn.xml @ 14:a0a8d77a991c draft
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author | florianbegusch |
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date | Thu, 03 Sep 2020 09:51:29 +0000 |
parents | f190567fe3f6 |
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--- a/qiime2/qiime_feature-classifier_fit-classifier-sklearn.xml Thu Sep 03 09:46:00 2020 +0000 +++ b/qiime2/qiime_feature-classifier_fit-classifier-sklearn.xml Thu Sep 03 09:51:29 2020 +0000 @@ -1,86 +1,66 @@ <?xml version="1.0" ?> -<tool id="qiime_feature-classifier_fit-classifier-sklearn" name="qiime feature-classifier fit-classifier-sklearn" version="2019.7"> - <description> - Train an almost arbitrary scikit-learn classifier</description> - <requirements> - <requirement type="package" version="2019.7">qiime2</requirement> - </requirements> - <command><![CDATA[ +<tool id="qiime_feature-classifier_fit-classifier-sklearn" name="qiime feature-classifier fit-classifier-sklearn" + version="2020.8"> + <description>Train an almost arbitrary scikit-learn classifier</description> + <requirements> + <requirement type="package" version="2020.8">qiime2</requirement> + </requirements> + <command><![CDATA[ qiime feature-classifier fit-classifier-sklearn --i-reference-reads=$ireferencereads +--i-reference-taxonomy=$ireferencetaxonomy -#if str( $id_to_taxonomy_fp.selector ) == 'history' -#set $tax = $id_to_taxonomy_fp.taxonomy_fp ---i-reference-taxonomy '$tax' -#else: -#set $tax = $id_to_taxonomy_fp.taxonomy_fp.fields.path ---i-reference-taxonomy '$tax' +#if str($iclassweight) != 'None': +--i-class-weight=$iclassweight #end if - ---p-classifier-specification="$pclassifierspecification" +--p-classifier-specification=$pclassifierspecification -#if str($iclassweight) != 'None': - --i-class-weight=$iclassweight +--o-classifier=oclassifier + +#if str($examples) != 'None': +--examples=$examples #end if ---o-classifier=oclassifier ; cp oclassifier.qza $oclassifier - ]]></command> - <inputs> - <param format="qza,no_unzip.zip" label="--i-reference-reads: ARTIFACT FeatureData[Sequence] [required]" name="ireferencereads" optional="False" type="data"/> - - <conditional name="id_to_taxonomy_fp" optional="True"> - <param name="selector" type="select" label="Reference taxonomy to query"> - <option value="cached">Public databases</option> - <option value="history">Databases from your history</option> - </param> - <when value="cached"> - <param argument="--taxonomy_fp" label="Reference taxonomy" type="select" optional="True"> - <options from_data_table="qiime_taxonomy" /> - </param> - </when> - <when value="history"> - <param argument="--taxonomy_fp" type="data" format="qza,no_unzip.zip" label="Reference databases" optional="True" /> - </when> - </conditional> - - <param label="--p-classifier-specification: TEXT [required]" name="pclassifierspecification" optional="False" type="text"/> - <param format="qza,no_unzip.zip" label="--i-class-weight: ARTIFACT FeatureTable[RelativeFrequency] [optional]" name="iclassweight" optional="True" type="data"/> - </inputs> - <outputs> - <data format="qza" label="${tool.name} on ${on_string}: classifier.qza" name="oclassifier"/> - </outputs> - <help><![CDATA[ -rain an almost arbitrary scikit-learn classifier -################################################ + + ]]></command> + <inputs> + <param format="qza,no_unzip.zip" label="--i-reference-reads: ARTIFACT FeatureData[Sequence] [required]" name="ireferencereads" optional="False" type="data" /> + <param format="qza,no_unzip.zip" label="--i-reference-taxonomy: ARTIFACT FeatureData[Taxonomy] [required]" name="ireferencetaxonomy" optional="False" type="data" /> + <param format="qza,no_unzip.zip" label="--i-class-weight: ARTIFACT FeatureTable[RelativeFrequency] [optional]" name="iclassweight" optional="False" type="data" /> + <param label="--p-classifier-specification: TEXT [required]" name="pclassifierspecification" optional="False" type="text" /> + <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" /> + + </inputs> + + <outputs> + <data format="qza" label="${tool.name} on ${on_string}: classifier.qza" name="oclassifier" /> + + </outputs> + + <help><![CDATA[ +Train an almost arbitrary scikit-learn classifier +############################################################### Train a scikit-learn classifier to classify reads. Parameters ---------- reference_reads : FeatureData[Sequence] - \ - reference_taxonomy : FeatureData[Taxonomy] - \ - classifier_specification : Str - \ - class_weight : FeatureTable[RelativeFrequency], optional - \ Returns ------- classifier : TaxonomicClassifier - \ - - ]]></help> -<macros> + ]]></help> + <macros> <import>qiime_citation.xml</import> -</macros> -<expand macro="qiime_citation"/> -</tool> + </macros> + <expand macro="qiime_citation"/> +</tool> \ No newline at end of file