diff qiime2/qiime_diversity_beta-group-significance.xml @ 14:a0a8d77a991c draft

Uploaded

--- a/qiime2/qiime_diversity_beta-group-significance.xml	Thu Sep 03 09:46:00 2020 +0000
+++ b/qiime2/qiime_diversity_beta-group-significance.xml	Thu Sep 03 09:51:29 2020 +0000
@@ -1,60 +1,107 @@
 <?xml version="1.0" ?>
-<tool id="qiime_diversity_beta-group-significance" name="qiime diversity beta-group-significance" version="2019.7">
-	<description> - Beta diversity group significance</description>
-	<requirements>
-		<requirement type="package" version="2019.7">qiime2</requirement>
-	</requirements>
-	<command><![CDATA[
+<tool id="qiime_diversity_beta-group-significance" name="qiime diversity beta-group-significance"
+      version="2020.8">
+  <description>Beta diversity group significance</description>
+  <requirements>
+    <requirement type="package" version="2020.8">qiime2</requirement>
+  </requirements>
+  <command><![CDATA[
 qiime diversity beta-group-significance
 
 --i-distance-matrix=$idistancematrix
---m-metadata-column="$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($pmethod) != 'None':
- --p-method=$pmethod
+--p-method=$pmethod
 #end if
 
 #if $ppairwise:
  --p-pairwise
 #end if
 
-#if str($ppermutations):
- --p-permutations=$ppermutations
+--p-permutations=$ppermutations
+
+--o-visualization=ovisualization
+
+#if str($examples) != 'None':
+--examples=$examples
 #end if
 
---o-visualization=ovisualization
+;
+cp odistancematrix.qza $odistancematrix
+
 ;
-qiime tools export --input-path ovisualization.qzv --output-path out   && mkdir -p '$ovisualization.files_path'
+qiime tools export  omantelscattervisualization.qzv --output-path out
+&& mkdir -p '$omantelscattervisualization.files_path'
+&& cp -r out/* '$omantelscattervisualization.files_path'
+&& mv '$omantelscattervisualization.files_path/index.html' '$omantelscattervisualization'
+
+;
+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-distance-matrix: ARTIFACT DistanceMatrix     Matrix of distances between pairs of samples. [required]" name="idistancematrix" optional="False" type="data"/>
-		<param label="--m-metadata-column: COLUMN  MetadataColumn[Categorical] Categorical sample metadata column.          [required]" name="mmetadatacolumn" optional="False" type="text"/>
-		<param label="--p-method: " name="pmethod" optional="True" type="select">
-			<option selected="True" value="None">Selection is Optional</option>
-			<option value="permanova">permanova</option>
-			<option value="anosim">anosim</option>
-			<option value="permdisp">permdisp</option>
-		</param>
-		<param label="--p-pairwise: --p-no-pairwise Perform pairwise tests between all pairs of groups in addition to the test across all groups. This can be very slow if there are a lot of groups in the metadata column.                                [default: False]" name="ppairwise" selected="False" type="boolean"/>
-		<param label="--p-permutations: INTEGER The number of permutations to be run when computing p-values.                                [default: 999]" name="ppermutations" optional="True" type="integer" value="999"/>
 
-		<param label="--m-metadata-file METADATA [required]" name="metadatafile" type="data" format="tabular,qza,no_unzip.zip" optional="False" />
-	</inputs>
-	<outputs>
-		<data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
-	</outputs>
-	<help><![CDATA[
+  ]]></command>
+  <inputs>
+    <param format="qza,no_unzip.zip" label="--i-distance-matrix: ARTIFACT DistanceMatrix     Matrix of distances between pairs of samples. [required]" name="idistancematrix" optional="False" type="data" />
+    <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file">
+      <param format="tabular,qza,no_unzip.zip" label="--m-metadata-file: METADATA" name="additional_input" optional="True" type="data" />
+    </repeat>
+    <param label="--m-metadata-column: COLUMN  MetadataColumn[Categorical] Categorical sample metadata column.          [required]" name="mmetadatacolumn" optional="False" type="text" />
+    <param label="--p-method: " name="pmethod" optional="True" type="select">
+      <option selected="True" value="None">Selection is Optional</option>
+      <option value="permanova">permanova</option>
+      <option value="anosim">anosim</option>
+      <option value="permdisp">permdisp</option>
+    </param>
+    <param label="--p-pairwise: --p-pairwise: / --p-no-pairwise Perform pairwise tests between all pairs of groups in addition to the test across all groups. This can be very slow if there are a lot of groups in the metadata column.                                [default: False]" name="ppairwise" selected="False" type="boolean" />
+    <param label="--p-permutations: INTEGER The number of permutations to be run when computing p-values.                                [default: 999]" name="ppermutations" optional="True" type="integer" value="999" />
+    <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
+    
+  </inputs>
+
+  <outputs>
+    <data format="html" label="${tool.name} on ${on_string}: visualization.html" name="ovisualization" />
+    
+  </outputs>
+
+  <help><![CDATA[
 Beta diversity group significance
-#################################
+###############################################################
 
 Determine whether groups of samples are significantly different from one
 another using a permutation-based statistical test.
@@ -77,9 +124,9 @@
 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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