Mercurial > repos > florianbegusch > qiime2_wrappers
diff qiime2/qiime_feature-classifier_classify-sklearn.xml @ 4:71f124e02000 draft default tip
Fixes
author | florianbegusch |
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date | Tue, 13 Aug 2019 07:40:25 -0400 |
parents | 149432539226 |
children |
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--- a/qiime2/qiime_feature-classifier_classify-sklearn.xml Wed Jul 17 01:53:11 2019 -0400 +++ b/qiime2/qiime_feature-classifier_classify-sklearn.xml Tue Aug 13 07:40:25 2019 -0400 @@ -7,8 +7,17 @@ <command><![CDATA[ qiime feature-classifier classify-sklearn + +#if str( $id_to_classifier_fp.selector ) == 'history' +#set $classifier = $id_to_classifier_fp.classifier_fp +--i-classifier '$classifier' +#else: +#set $classifier = $id_to_classifier_fp.classifier_fp.fields.path +--i-classifier '$classifier' +#end if + + --i-reads=$ireads ---i-classifier=$iclassifier #set $pnjobs = '${GALAXY_SLOTS:-4}' @@ -17,8 +26,10 @@ #end if -#if $pconfidence: - --p-confidence=$pconfidence +#if str($pconfidence) != '': + #if float($pconfidence) >= 0.0: + --p-confidence=$pconfidence + #end if #end if #if str($preadorientation) != 'None': @@ -30,8 +41,22 @@ cp oclassification.qza $oclassification ]]></command> <inputs> + <conditional name="id_to_classifier_fp" optional="True"> + <param name="selector" type="select" label="Reference classifier to query"> + <option value="cached">Public classifiers</option> + <option value="history">Classifiers from your history</option> + </param> + <when value="cached"> + <param name="classifier_fp" label="Reference classifier" type="select" optional="True"> + <options from_data_table="qiime_rep_set" /> + </param> + </when> + <when value="history"> + <param name="classifier_fp" type="data" format="qza,no_unzip.zip" label="Reference classifier" optional="True" /> + </when> + </conditional> + <param format="qza,no_unzip.zip" label="--i-reads: ARTIFACT FeatureData[Sequence] The feature data to be classified. [required]" name="ireads" optional="False" type="data"/> - <param format="qza,no_unzip.zip" label="--i-classifier: ARTIFACT TaxonomicClassifier The taxonomic classifier for classifying the reads. [required]" name="iclassifier" optional="False" type="data"/> <param label="--p-confidence: NUMBER Confidence threshold for limiting taxonomic depth. Provide -1 to disable confidence calculation, or 0 to calculate confidence but not apply it to limit the taxonomic depth of the assignments. [default: 0.7]" name="pconfidence" optional="True" type="float" value="0.7"/> <param label="--p-read-orientation: " name="preadorientation" optional="True" type="select"> <option selected="True" value="None">Selection is Optional</option>