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comparison qiime2/qiime_sample-classifier_regress-samples.xml @ 4:71f124e02000 draft default tip

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Fixes
author florianbegusch
date Tue, 13 Aug 2019 07:40:25 -0400
parents 149432539226
children
comparison
equal deleted inserted replaced
3:eda5df31da55 4:71f124e02000
8 qiime sample-classifier regress-samples 8 qiime sample-classifier regress-samples
9 9
10 --i-table=$itable 10 --i-table=$itable
11 --m-metadata-column="$mmetadatacolumn" 11 --m-metadata-column="$mmetadatacolumn"
12 12
13 #if $ptestsize: 13 #if str($ptestsize):
14 --p-test-size=$ptestsize 14 --p-test-size=$ptestsize
15 #end if 15 #end if
16 16
17 #if $pstep: 17 #if str($pstep):
18 --p-step=$pstep 18 --p-step=$pstep
19 #end if 19 #end if
20 20
21 #if $pcv: 21 #if str($pcv):
22 --p-cv=$pcv 22 --p-cv=$pcv
23 #end if 23 #end if
24 24
25 #if str($prandomstate): 25 #if str($prandomstate):
26 --p-random-state="$prandomstate" 26 --p-random-state="$prandomstate"
31 #if str($pnjobs): 31 #if str($pnjobs):
32 --p-n-jobs="$pnjobs" 32 --p-n-jobs="$pnjobs"
33 #end if 33 #end if
34 34
35 35
36 #if $pnestimators: 36 #if str($pnestimators):
37 --p-n-estimators=$pnestimators 37 --p-n-estimators=$pnestimators
38 #end if 38 #end if
39 39
40 #if str($pestimator) != 'None': 40 #if str($pestimator) != 'None':
41 --p-estimator=$pestimator 41 --p-estimator=$pestimator
56 #if str($pmissingsamples) != 'None': 56 #if str($pmissingsamples) != 'None':
57 --p-missing-samples=$pmissingsamples 57 --p-missing-samples=$pmissingsamples
58 #end if 58 #end if
59 59
60 60
61 #if $input_files_mmetadatafile: 61
62 #def list_dict_to_string(list_dict): 62
63 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name') 63 #if $metadatafile:
64 #for d in list_dict[1:]: 64 --m-metadata-file=$metadatafile
65 #set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
66 #end for
67 #return $file_list
68 #end def
69 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
70 #end if 65 #end if
66
67
71 68
72 69
73 --o-sample-estimator=osampleestimator 70 --o-sample-estimator=osampleestimator
74 --o-feature-importance=ofeatureimportance 71 --o-feature-importance=ofeatureimportance
75 --o-predictions=opredictions 72 --o-predictions=opredictions
87 && mv '$oaccuracyresults.files_path/index.html' '$oaccuracyresults' 84 && mv '$oaccuracyresults.files_path/index.html' '$oaccuracyresults'
88 ]]></command> 85 ]]></command>
89 <inputs> 86 <inputs>
90 <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"/> 87 <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"/>
91 <param label="--m-metadata-column: COLUMN MetadataColumn[Numeric] Numeric metadata column to use as prediction target. [required]" name="mmetadatacolumn" optional="False" type="text"/> 88 <param label="--m-metadata-column: COLUMN MetadataColumn[Numeric] Numeric metadata column to use as prediction target. [required]" name="mmetadatacolumn" optional="False" type="text"/>
92 <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"/> 89 <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" />
93 <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"/> 90 <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" />
94 <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"/> 91 <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"/>
95 <param label="--p-random-state: INTEGER Seed used by random number generator. [optional]" name="prandomstate" optional="True" type="integer"/> 92 <param label="--p-random-state: INTEGER Seed used by random number generator. [optional]" name="prandomstate" optional="True" type="integer"/>
96 <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"/> 93 <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"/>
97 <param label="--p-estimator: " name="pestimator" optional="True" type="select"> 94 <param label="--p-estimator: " name="pestimator" optional="True" type="select">
98 <option selected="True" value="None">Selection is Optional</option> 95 <option selected="True" value="None">Selection is Optional</option>
99 <option value="RandomForestRegressor">RandomForestRegressor</option> 96 <option value="RandomForestRegressor">RandomForestRegressor</option>
114 <option selected="True" value="None">Selection is Optional</option> 111 <option selected="True" value="None">Selection is Optional</option>
115 <option value="error">error</option> 112 <option value="error">error</option>
116 <option value="ignore">ignore</option> 113 <option value="ignore">ignore</option>
117 </param> 114 </param>
118 115
119 <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file"> 116
120 <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" /> 117 <param label="--m-metadata-file METADATA" name="metadatafile" type="data" format="tabular,qza,no_unzip.zip" />
121 </repeat> 118
122 119
123 </inputs> 120 </inputs>
124 <outputs> 121 <outputs>
125 <data format="qza" label="${tool.name} on ${on_string}: sampleestimator.qza" name="osampleestimator"/> 122 <data format="qza" label="${tool.name} on ${on_string}: sampleestimator.qza" name="osampleestimator"/>
126 <data format="qza" label="${tool.name} on ${on_string}: featureimportance.qza" name="ofeatureimportance"/> 123 <data format="qza" label="${tool.name} on ${on_string}: featureimportance.qza" name="ofeatureimportance"/>