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diff qiime2/qiime_sample-classifier_split-table.xml @ 14:a0a8d77a991c draft

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Uploaded
author florianbegusch
date Thu, 03 Sep 2020 09:51:29 +0000
parents f190567fe3f6
children
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--- a/qiime2/qiime_sample-classifier_split-table.xml	Thu Sep 03 09:46:00 2020 +0000
+++ b/qiime2/qiime_sample-classifier_split-table.xml	Thu Sep 03 09:51:29 2020 +0000
@@ -1,68 +1,101 @@
 <?xml version="1.0" ?>
-<tool id="qiime_sample-classifier_split-table" name="qiime sample-classifier split-table" version="2019.7">
-	<description> - Split a feature table into training and testing sets.</description>
-	<requirements>
-		<requirement type="package" version="2019.7">qiime2</requirement>
-	</requirements>
-	<command><![CDATA[
+<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=$itable
---m-metadata-column="$mmetadatacolumn"
-
+# 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 $metadatafile:
- --m-metadata-file=$metadatafile
+#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
 
 
-
-#if str($ptestsize):
- --p-test-size=$ptestsize
-#end if
+--p-test-size=$ptestsize
 
 #if str($prandomstate):
- --p-random-state="$prandomstate"
+  --p-random-state=$prandomstate
 #end if
-
 #if $pnostratify:
  --p-no-stratify
 #end if
 
 #if str($pmissingsamples) != 'None':
- --p-missing-samples=$pmissingsamples
+--p-missing-samples=$pmissingsamples
 #end if
 
 --o-training-table=otrainingtable
+
 --o-test-table=otesttable
+
+#if str($examples) != 'None':
+--examples=$examples
+#end if
+
 ;
-cp otrainingtable.qza $otrainingtable;
-cp otesttable.qza $otesttable;
-	]]></command>
-	<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 | Categorical] 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" min="0" max="1" exclusive_end="True"/>
-		<param label="--p-random-state: INTEGER Seed used by random number generator.        [optional]" name="prandomstate" optional="True" type="integer"/>
-		<param label="--p-no-stratify: Evenly stratify training and test data among metadata categories. If True, all values in column must match at least two samples.                      [default: False]" 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>
+cp otesttable.qza $otesttable
 
-		<param label="--m-metadata-file METADATA" name="metadatafile" type="data" format="tabular,qza,no_unzip.zip" />
+  ]]></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>
 
-	</inputs>
-	<outputs>
-		<data format="qza" label="${tool.name} on ${on_string}: trainingtable.qza" name="otrainingtable"/>
-		<data format="qza" label="${tool.name} on ${on_string}: testtable.qza" name="otesttable"/>
-	</outputs>
-	<help><![CDATA[
+  <outputs>
+    <data format="qza" label="${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
@@ -70,7 +103,7 @@
 
 Parameters
 ----------
-table : FeatureTable[Frequency]
+table : FeatureTable[Frequency¹ | RelativeFrequency² | PresenceAbsence³ | Balance⁴ | PercentileNormalized⁵ | Design⁶]
     Feature table containing all features that should be used for target
     prediction.
 metadata : MetadataColumn[Numeric | Categorical]
@@ -91,13 +124,13 @@
 
 Returns
 -------
-training_table : FeatureTable[Frequency]
+training_table : FeatureTable[Frequency¹ | RelativeFrequency² | PresenceAbsence³ | Balance⁴ | PercentileNormalized⁵ | Design⁶]
     Feature table containing training samples
-test_table : FeatureTable[Frequency]
+test_table : FeatureTable[Frequency¹ | RelativeFrequency² | PresenceAbsence³ | Balance⁴ | PercentileNormalized⁵ | Design⁶]
     Feature table containing test samples
-	]]></help>
-<macros>
+  ]]></help>
+  <macros>
     <import>qiime_citation.xml</import>
-</macros>
-<expand macro="qiime_citation"/>
-</tool>
+  </macros>
+  <expand macro="qiime_citation"/>
+</tool>
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