Mercurial > repos > florianbegusch > qiime2_wrappers
diff qiime2/qiime_sample-classifier_regress-samples.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_sample-classifier_regress-samples.xml Wed Jul 17 01:53:11 2019 -0400 +++ b/qiime2/qiime_sample-classifier_regress-samples.xml Tue Aug 13 07:40:25 2019 -0400 @@ -10,15 +10,15 @@ --i-table=$itable --m-metadata-column="$mmetadatacolumn" -#if $ptestsize: +#if str($ptestsize): --p-test-size=$ptestsize #end if -#if $pstep: +#if str($pstep): --p-step=$pstep #end if -#if $pcv: +#if str($pcv): --p-cv=$pcv #end if @@ -33,7 +33,7 @@ #end if -#if $pnestimators: +#if str($pnestimators): --p-n-estimators=$pnestimators #end if @@ -58,18 +58,15 @@ #end if -#if $input_files_mmetadatafile: -#def list_dict_to_string(list_dict): - #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name') - #for d in list_dict[1:]: - #set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name') - #end for - #return $file_list -#end def - --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile) + + +#if $metadatafile: + --m-metadata-file=$metadatafile #end if + + --o-sample-estimator=osampleestimator --o-feature-importance=ofeatureimportance --o-predictions=opredictions @@ -89,9 +86,9 @@ <inputs> <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] Feature table containing all features that should be used for target prediction. [required]" name="itable" optional="False" type="data"/> <param label="--m-metadata-column: COLUMN MetadataColumn[Numeric] Numeric metadata column to use as prediction target. [required]" name="mmetadatacolumn" optional="False" type="text"/> - <param label="--p-test-size: PROPORTION Range(0.0, 1.0, inclusive_start=False) Fraction of input samples to exclude from training set and use for classifier testing. [default: 0.2]" name="ptestsize" optional="True" type="float" value="0.2"/> - <param label="--p-step: PROPORTION Range(0.0, 1.0, inclusive_start=False) If optimize-feature-selection is True, step is the percentage of features to remove at each iteration. [default: 0.05]" name="pstep" optional="True" type="float" value="0.05"/> - <param label="--p-cv: INTEGER Number of k-fold cross-validations to perform. Range(1, None) [default: 5]" name="pcv" optional="True" type="integer" value="5"/> + <param label="--p-test-size: PROPORTION Range(0.0, 1.0, inclusive_start=False) Fraction of input samples to exclude from training set and use for classifier testing. [default: 0.2]" name="ptestsize" optional="True" type="float" value="0.2" min="0" max="1" /> + <param label="--p-step: PROPORTION Range(0.0, 1.0, inclusive_start=False) If optimize-feature-selection is True, step is the percentage of features to remove at each iteration. [default: 0.05]" name="pstep" optional="True" type="float" value="0.05" min="0" max="1" /> + <param label="--p-cv: INTEGER Number of k-fold cross-validations to perform. Range(1, None) [default: 5]" name="pcv" optional="True" type="integer" value="5" min="1"/> <param label="--p-random-state: INTEGER Seed used by random number generator. [optional]" name="prandomstate" optional="True" type="integer"/> <param label="--p-n-estimators: INTEGER Range(1, None) Number of trees to grow for estimation. More trees will improve predictive accuracy up to a threshold level, but will also increase time and memory requirements. This parameter only affects ensemble estimators, such as Random Forest, AdaBoost, ExtraTrees, and GradientBoosting. [default: 100]" name="pnestimators" optional="True" type="integer" value="100" min="1"/> <param label="--p-estimator: " name="pestimator" optional="True" type="select"> @@ -116,9 +113,9 @@ <option value="ignore">ignore</option> </param> - <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file"> - <param label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [optional]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" /> - </repeat> + + <param label="--m-metadata-file METADATA" name="metadatafile" type="data" format="tabular,qza,no_unzip.zip" /> + </inputs> <outputs>