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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2-2020.8/qiime_composition_ancom.xml	Fri Sep 04 12:44:24 2020 +0000
@@ -0,0 +1,126 @@
+<?xml version="1.0" ?>
+<tool id="qiime_composition_ancom" name="qiime composition ancom"
+      version="2020.8">
+  <description>Apply ANCOM to identify features that differ in abundance.</description>
+  <requirements>
+    <requirement type="package" version="2020.8">qiime2</requirement>
+  </requirements>
+  <command><![CDATA[
+qiime composition ancom
+
+--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
+
+
+#if str($ptransformfunction) != 'None':
+--p-transform-function=$ptransformfunction
+#end if
+
+#if str($pdifferencefunction) != 'None':
+--p-difference-function=$pdifferencefunction
+#end if
+
+--o-visualization=ovisualization
+
+#if str($examples) != 'None':
+--examples=$examples
+#end if
+
+;
+cp ocompositiontable.qza $ocompositiontable
+
+;
+qiime tools export  ovisualization.qzv --output-path out
+&& mkdir -p '$ovisualization.files_path'
+&& cp -r out/* '$ovisualization.files_path'
+&& mv '$ovisualization.files_path/index.html' '$ovisualization'
+
+  ]]></command>
+  <inputs>
+    <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Composition] The feature table to be used for ANCOM computation. [required]" name="itable" optional="False" type="data" />
+    <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file">
+      <param format="tabular,qza,no_unzip.zip" label="--m-metadata-file: METADATA" name="additional_input" optional="True" type="data" />
+    </repeat>
+    <param label="--m-metadata-column: COLUMN  MetadataColumn[Categorical] The categorical sample metadata column to test for differential abundance across.               [required]" name="mmetadatacolumn" optional="False" type="text" />
+    <param label="--p-transform-function: " name="ptransformfunction" optional="True" type="select">
+      <option selected="True" value="None">Selection is Optional</option>
+      <option value="sqrt">sqrt</option>
+      <option value="log">log</option>
+      <option value="clr">clr</option>
+    </param>
+    <param label="--p-difference-function: " name="pdifferencefunction" optional="True" type="select">
+      <option selected="True" value="None">Selection is Optional</option>
+      <option value="mean_difference">mean_difference</option>
+      <option value="f_statistic">f_statistic</option>
+    </param>
+    <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
+    
+  </inputs>
+
+  <outputs>
+    <data format="html" label="${tool.name} on ${on_string}: visualization.html" name="ovisualization" />
+    
+  </outputs>
+
+  <help><![CDATA[
+Apply ANCOM to identify features that differ in abundance.
+###############################################################
+
+Apply Analysis of Composition of Microbiomes (ANCOM) to identify features
+that are differentially abundant across groups.
+
+Parameters
+----------
+table : FeatureTable[Composition]
+    The feature table to be used for ANCOM computation.
+metadata : MetadataColumn[Categorical]
+    The categorical sample metadata column to test for differential
+    abundance across.
+transform_function : Str % Choices('sqrt', 'log', 'clr'), optional
+    The method applied to transform feature values before generating
+    volcano plots.
+difference_function : Str % Choices('mean_difference', 'f_statistic'), optional
+    The method applied to visualize fold difference in feature abundances
+    across groups for volcano plots.
+
+Returns
+-------
+visualization : Visualization
+  ]]></help>
+  <macros>
+    <import>qiime_citation.xml</import>
+  </macros>
+  <expand macro="qiime_citation"/>
+</tool>
\ No newline at end of file