--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_feature-table_group.xml	Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,119 @@
+<?xml version="1.0" ?>
+<tool id="qiime_feature-table_group" name="qiime feature-table group"
+      version="2020.8">
+  <description>Group samples or features by a metadata column</description>
+  <requirements>
+    <requirement type="package" version="2020.8">qiime2</requirement>
+  </requirements>
+  <command><![CDATA[
+qiime feature-table group
+
+--i-table=$itable
+
+--p-axis=$paxis
+# 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-mode=$pmode
+
+--o-grouped-table=ogroupedtable
+
+#if str($examples) != 'None':
+--examples=$examples
+#end if
+
+;
+cp ogroupedtable.qza $ogroupedtable
+
+  ]]></command>
+  <inputs>
+    <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] The table to group samples or features on.   [required]" name="itable" optional="False" type="data" />
+    <param label="--p-axis: " name="paxis" optional="False" type="select">
+      <option value="sample">sample</option>
+      <option value="feature">feature</option>
+    </param>
+    <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file">
+      <param format="tabular,qza,no_unzip.zip" label="--m-metadata-file: METADATA" name="additional_input" optional="True" type="data" />
+    </repeat>
+    <param label="--m-metadata-column: COLUMN  MetadataColumn[Categorical] A column defining the groups. Each unique value will become a new ID for the table on the given `axis`. [required]" name="mmetadatacolumn" optional="False" type="text" />
+    <param label="--p-mode: " name="pmode" optional="False" type="select">
+      <option value="sum">sum</option>
+      <option value="mean-ceiling">mean-ceiling</option>
+      <option value="median-ceiling">median-ceiling</option>
+    </param>
+    <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
+    
+  </inputs>
+
+  <outputs>
+    <data format="qza" label="${tool.name} on ${on_string}: groupedtable.qza" name="ogroupedtable" />
+    
+  </outputs>
+
+  <help><![CDATA[
+Group samples or features by a metadata column
+###############################################################
+
+Group samples or features in a feature table using metadata to define the
+mapping of IDs to a group.
+
+Parameters
+----------
+table : FeatureTable[Frequency]
+    The table to group samples or features on.
+axis : Str % Choices('sample', 'feature')
+    Along which axis to group. Each ID in the given axis must exist in
+    `metadata`.
+metadata : MetadataColumn[Categorical]
+    A column defining the groups. Each unique value will become a new ID
+    for the table on the given `axis`.
+mode : Str % Choices('sum', 'mean-ceiling', 'median-ceiling')
+    How to combine samples or features within a group. `sum` will sum the
+    frequencies across all samples or features within a group; `mean-
+    ceiling` will take the ceiling of the mean of these frequencies;
+    `median-ceiling` will take the ceiling of the median of these
+    frequencies.
+
+Returns
+-------
+grouped_table : FeatureTable[Frequency]
+    A table that has been grouped along the given `axis`. IDs on that axis
+    are replaced by values in the `metadata` column.
+  ]]></help>
+  <macros>
+    <import>qiime_citation.xml</import>
+  </macros>
+  <expand macro="qiime_citation"/>
+</tool>
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