diff qiime2-2020.8/qiime_sample-classifier_split-table.xml @ 20:d93d8888f0b0 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2-2020.8/qiime_sample-classifier_split-table.xml	Fri Sep 04 12:44:24 2020 +0000
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+<?xml version="1.0" ?>
+<tool id="qiime_sample-classifier_split-table" name="qiime sample-classifier split-table"
+      version="2020.8">
+  <description>Split a feature table into training and testing sets.</description>
+  <requirements>
+    <requirement type="package" version="2020.8">qiime2</requirement>
+  </requirements>
+  <command><![CDATA[
+qiime sample-classifier split-table
+
+--i-table=$itable
+# 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($input_files_mmetadatafile)
+# end if
+
+#if '__ob__' in str($mmetadatacolumn):
+  #set $mmetadatacolumn_temp = $mmetadatacolumn.replace('__ob__', '[')
+  #set $mmetadatacolumn = $mmetadatacolumn_temp
+#end if
+#if '__cb__' in str($mmetadatacolumn):
+  #set $mmetadatacolumn_temp = $mmetadatacolumn.replace('__cb__', ']')
+  #set $mmetadatacolumn = $mmetadatacolumn_temp
+#end if
+#if 'X' in str($mmetadatacolumn):
+  #set $mmetadatacolumn_temp = $mmetadatacolumn.replace('X', '\\')
+  #set $mmetadatacolumn = $mmetadatacolumn_temp
+#end if
+#if '__sq__' in str($mmetadatacolumn):
+  #set $mmetadatacolumn_temp = $mmetadatacolumn.replace('__sq__', "'")
+  #set $mmetadatacolumn = $mmetadatacolumn_temp
+#end if
+#if '__db__' in str($mmetadatacolumn):
+  #set $mmetadatacolumn_temp = $mmetadatacolumn.replace('__db__', '"')
+  #set $mmetadatacolumn = $mmetadatacolumn_temp
+#end if
+
+--m-metadata-column=$mmetadatacolumn
+
+
+--p-test-size=$ptestsize
+
+#if str($prandomstate):
+  --p-random-state=$prandomstate
+#end if
+#if $pnostratify:
+ --p-no-stratify
+#end if
+
+#if str($pmissingsamples) != 'None':
+--p-missing-samples=$pmissingsamples
+#end if
+
+--o-training-table=otrainingtable
+
+--o-test-table=otesttable
+
+#if str($examples) != 'None':
+--examples=$examples
+#end if
+
+;
+cp otesttable.qza $otesttable
+
+  ]]></command>
+  <inputs>
+    <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency¹ | RelativeFrequency² | PresenceAbsence³ | Balance⁴ | PercentileNormalized⁵ | Design⁶] Feature table containing all features that should be used for target prediction.                  [required]" name="itable" optional="False" type="data" />
+    <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file">
+      <param format="tabular,qza,no_unzip.zip" label="--m-metadata-file: METADATA" name="additional_input" optional="True" type="data" />
+    </repeat>
+    <param label="--m-metadata-column: COLUMN  MetadataColumn[Numeric | Categorical] Numeric metadata column to use as prediction target. [required]" name="mmetadatacolumn" optional="False" type="text" />
+    <param exclude_min="True" label="--p-test-size: PROPORTION Range(0.0, 1.0, inclusive_start=False) Fraction of input samples to exclude from training set and use for classifier testing.          [default: 0.2]" max="1.0" min="0.0" name="ptestsize" optional="True" type="float" value="0.2" />
+    <param label="--p-random-state: INTEGER Seed used by random number generator.        [optional]" name="prandomstate" optional="False" type="text" />
+    <param label="--p-no-stratify: Do not evenly stratify training and test data among metadata categories. If True, all values in column must match at least two samples.                      [default: True]" name="pnostratify" selected="False" type="boolean" />
+    <param label="--p-missing-samples: " name="pmissingsamples" optional="True" type="select">
+      <option selected="True" value="None">Selection is Optional</option>
+      <option value="error">error</option>
+      <option value="ignore">ignore</option>
+    </param>
+    <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
+    
+  </inputs>
+
+  <outputs>
+    <data format="qza" label="${tool.name} on ${on_string}: trainingtable.qza" name="otrainingtable" />
+    <data format="qza" label="${tool.name} on ${on_string}: testtable.qza" name="otesttable" />
+    
+  </outputs>
+
+  <help><![CDATA[
+Split a feature table into training and testing sets.
+###############################################################
+
+Split a feature table into training and testing sets. By default stratifies
+training and test sets on a metadata column, such that values in that
+column are evenly represented across training and test sets.
+
+Parameters
+----------
+table : FeatureTable[Frequency¹ | RelativeFrequency² | PresenceAbsence³ | Balance⁴ | PercentileNormalized⁵ | Design⁶]
+    Feature table containing all features that should be used for target
+    prediction.
+metadata : MetadataColumn[Numeric | Categorical]
+    Numeric metadata column to use as prediction target.
+test_size : Float % Range(0.0, 1.0, inclusive_start=False), optional
+    Fraction of input samples to exclude from training set and use for
+    classifier testing.
+random_state : Int, optional
+    Seed used by random number generator.
+stratify : Bool, optional
+    Evenly stratify training and test data among metadata categories. If
+    True, all values in column must match at least two samples.
+missing_samples : Str % Choices('error', 'ignore'), optional
+    How to handle missing samples in metadata. "error" will fail if missing
+    samples are detected. "ignore" will cause the feature table and
+    metadata to be filtered, so that only samples found in both files are
+    retained.
+
+Returns
+-------
+training_table : FeatureTable[Frequency¹ | RelativeFrequency² | PresenceAbsence³ | Balance⁴ | PercentileNormalized⁵ | Design⁶]
+    Feature table containing training samples
+test_table : FeatureTable[Frequency¹ | RelativeFrequency² | PresenceAbsence³ | Balance⁴ | PercentileNormalized⁵ | Design⁶]
+    Feature table containing test samples
+  ]]></help>
+  <macros>
+    <import>qiime_citation.xml</import>
+  </macros>
+  <expand macro="qiime_citation"/>
+</tool>
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