diff qiime2-2020.8/qiime_feature-table_merge.xml @ 20:d93d8888f0b0 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2-2020.8/qiime_feature-table_merge.xml	Fri Sep 04 12:44:24 2020 +0000
@@ -0,0 +1,76 @@
+<?xml version="1.0" ?>
+<tool id="qiime_feature-table_merge" name="qiime feature-table merge"
+      version="2020.8">
+  <description>Combine multiple tables</description>
+  <requirements>
+    <requirement type="package" version="2020.8">qiime2</requirement>
+  </requirements>
+  <command><![CDATA[
+qiime feature-table merge
+# if $input_files_itables:
+  # 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 + ' --i-tables=' + d['additional_input'].__getattr__('file_name')
+    # end for
+    # return $file_list
+  # end def
+--i-tables=$list_dict_to_string($input_files_itables)
+# end if
+
+#if str($poverlapmethod) != 'None':
+--p-overlap-method=$poverlapmethod
+#end if
+
+--o-merged-table=omergedtable
+
+#if str($examples) != 'None':
+--examples=$examples
+#end if
+
+;
+cp omergedtable.qza $omergedtable
+
+  ]]></command>
+  <inputs>
+    <repeat name="input_files_itables" optional="False" title="--i-tables">
+      <param format="qza,no_unzip.zip" label="--i-tables: ARTIFACTS... List[FeatureTable[Frequency]] The collection of feature tables to be merged. [required]" name="additional_input" optional="False" type="data" />
+    </repeat>
+    <param label="--p-overlap-method: " name="poverlapmethod" optional="True" type="select">
+      <option selected="True" value="None">Selection is Optional</option>
+      <option value="error_on_overlapping_sample">error_on_overlapping_sample</option>
+      <option value="error_on_overlapping_feature">error_on_overlapping_feature</option>
+      <option value="sum">sum</option>
+    </param>
+    <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
+    
+  </inputs>
+
+  <outputs>
+    <data format="qza" label="${tool.name} on ${on_string}: mergedtable.qza" name="omergedtable" />
+    
+  </outputs>
+
+  <help><![CDATA[
+Combine multiple tables
+###############################################################
+
+Combines feature tables using the `overlap_method` provided.
+
+Parameters
+----------
+tables : List[FeatureTable[Frequency]]
+    The collection of feature tables to be merged.
+overlap_method : Str % Choices('error_on_overlapping_sample', 'error_on_overlapping_feature', 'sum'), optional
+    Method for handling overlapping ids.
+
+Returns
+-------
+merged_table : FeatureTable[Frequency]
+    The resulting merged feature table.
+  ]]></help>
+  <macros>
+    <import>qiime_citation.xml</import>
+  </macros>
+  <expand macro="qiime_citation"/>
+</tool>
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