diff qiime2/qiime_composition_ancom.xml @ 14:a0a8d77a991c draft

Uploaded

--- a/qiime2/qiime_composition_ancom.xml	Thu Sep 03 09:46:00 2020 +0000
+++ b/qiime2/qiime_composition_ancom.xml	Thu Sep 03 09:51:29 2020 +0000
@@ -1,64 +1,102 @@
 <?xml version="1.0" ?>
-<tool id="qiime_composition_ancom" name="qiime composition ancom" version="2019.7">
-	<description> - Apply ANCOM to identify features that differ in abundance.</description>
-	<requirements>
-		<requirement type="package" version="2019.7">qiime2</requirement>
-	</requirements>
-	<command><![CDATA[
+<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 $metadatafile:
- --m-metadata-file=$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="$mmetadatacolumn"
+--m-metadata-column=$mmetadatacolumn
 
-#if str($pdifferencefunction) != 'None':
---p-difference-function=$pdifferencefunction
-#end if
 
 #if str($ptransformfunction) != 'None':
 --p-transform-function=$ptransformfunction
 #end if
 
---o-visualization=ovisualization;
+#if str($pdifferencefunction) != 'None':
+--p-difference-function=$pdifferencefunction
+#end if
+
+--o-visualization=ovisualization
 
-qiime tools export --input-path ovisualization.qzv --output-path out   && mkdir -p '$ovisualization.files_path'
+#if str($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: FeatureTable[Composition] - The feature table to be used for ANCOM computation.  [required]" name="itable" optional="False" type="data"/>
-
-		<param label="--m-metadata-file METADATA" name="metadatafile" type="data" format="tabular,qza,no_unzip.zip" optional="True" />
-
 
-		<param label="--m-metadata-column: MetadataColumn[Categorical] - Column from metadata file or artifact viewable as metadata. The categorical sample metadata column to test for differential abundance across.  [required]" name="mmetadatacolumn" optional="False" type="text"/>
-		<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="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
-		<param label="--p-transform-function: " name="ptransformfunction" optional="True" type="select">
-			<option selected="True" value="None">Selection is Optional</option>
-			<option value="log">log</option>
-			<option value="clr">clr</option>
-			<option value="sqrt">sqrt</option>
-		</param>
-	</inputs>
-	<outputs>
-		<data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
-	</outputs>
-	<help><![CDATA[
+  ]]></command>
+  <inputs>
+    <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Composition] The feature table to be used for ANCOM computation. [required]" name="itable" optional="False" type="data" />
+    <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file">
+      <param format="tabular,qza,no_unzip.zip" label="--m-metadata-file: METADATA" name="additional_input" optional="True" type="data" />
+    </repeat>
+    <param label="--m-metadata-column: COLUMN  MetadataColumn[Categorical] The categorical sample metadata column to test for differential abundance across.               [required]" name="mmetadatacolumn" optional="False" type="text" />
+    <param label="--p-transform-function: " name="ptransformfunction" optional="True" type="select">
+      <option selected="True" value="None">Selection is Optional</option>
+      <option value="sqrt">sqrt</option>
+      <option value="log">log</option>
+      <option value="clr">clr</option>
+    </param>
+    <param label="--p-difference-function: " name="pdifferencefunction" optional="True" type="select">
+      <option selected="True" value="None">Selection is Optional</option>
+      <option value="mean_difference">mean_difference</option>
+      <option value="f_statistic">f_statistic</option>
+    </param>
+    <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
+    
+  </inputs>
+
+  <outputs>
+    <data format="html" label="${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.
@@ -80,9 +118,9 @@
 Returns
 -------
 visualization : Visualization
-	]]></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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