diff qiime2/qiime_longitudinal_volatility.xml @ 14:a0a8d77a991c draft

Uploaded

--- a/qiime2/qiime_longitudinal_volatility.xml	Thu Sep 03 09:46:00 2020 +0000
+++ b/qiime2/qiime_longitudinal_volatility.xml	Thu Sep 03 09:51:29 2020 +0000
@@ -1,87 +1,170 @@
 <?xml version="1.0" ?>
-<tool id="qiime_longitudinal_volatility" name="qiime longitudinal volatility" version="2019.7">
-	<description> - Generate interactive volatility plot</description>
-	<requirements>
-		<requirement type="package" version="2019.7">qiime2</requirement>
-	</requirements>
-	<command><![CDATA[
+<tool id="qiime_longitudinal_volatility" name="qiime longitudinal volatility"
+      version="2020.8">
+  <description>Generate interactive volatility plot</description>
+  <requirements>
+    <requirement type="package" version="2020.8">qiime2</requirement>
+  </requirements>
+  <command><![CDATA[
 qiime longitudinal volatility
 
---p-state-column="$pstatecolumn"
+#if str($itable) != 'None':
+--i-table=$itable
+#end if
+# 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 str($itable) != 'None':
- --i-table=$itable
+#if '__ob__' in str($pstatecolumn):
+  #set $pstatecolumn_temp = $pstatecolumn.replace('__ob__', '[')
+  #set $pstatecolumn = $pstatecolumn_temp
+#end if
+#if '__cb__' in str($pstatecolumn):
+  #set $pstatecolumn_temp = $pstatecolumn.replace('__cb__', ']')
+  #set $pstatecolumn = $pstatecolumn_temp
+#end if
+#if 'X' in str($pstatecolumn):
+  #set $pstatecolumn_temp = $pstatecolumn.replace('X', '\\')
+  #set $pstatecolumn = $pstatecolumn_temp
+#end if
+#if '__sq__' in str($pstatecolumn):
+  #set $pstatecolumn_temp = $pstatecolumn.replace('__sq__', "'")
+  #set $pstatecolumn = $pstatecolumn_temp
+#end if
+#if '__db__' in str($pstatecolumn):
+  #set $pstatecolumn_temp = $pstatecolumn.replace('__db__', '"')
+  #set $pstatecolumn = $pstatecolumn_temp
 #end if
 
+--p-state-column=$pstatecolumn
 
 
+#if '__ob__' in str($pindividualidcolumn):
+  #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('__ob__', '[')
+  #set $pindividualidcolumn = $pindividualidcolumn_temp
+#end if
+#if '__cb__' in str($pindividualidcolumn):
+  #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('__cb__', ']')
+  #set $pindividualidcolumn = $pindividualidcolumn_temp
+#end if
+#if 'X' in str($pindividualidcolumn):
+  #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('X', '\\')
+  #set $pindividualidcolumn = $pindividualidcolumn_temp
+#end if
 #if '__sq__' in str($pindividualidcolumn):
   #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('__sq__', "'")
   #set $pindividualidcolumn = $pindividualidcolumn_temp
 #end if
+#if '__db__' in str($pindividualidcolumn):
+  #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('__db__', '"')
+  #set $pindividualidcolumn = $pindividualidcolumn_temp
+#end if
 
 #if str($pindividualidcolumn):
- --p-individual-id-column="$pindividualidcolumn"
+  --p-individual-id-column=$pindividualidcolumn
 #end if
 
-
+#if '__ob__' in str($pdefaultgroupcolumn):
+  #set $pdefaultgroupcolumn_temp = $pdefaultgroupcolumn.replace('__ob__', '[')
+  #set $pdefaultgroupcolumn = $pdefaultgroupcolumn_temp
+#end if
+#if '__cb__' in str($pdefaultgroupcolumn):
+  #set $pdefaultgroupcolumn_temp = $pdefaultgroupcolumn.replace('__cb__', ']')
+  #set $pdefaultgroupcolumn = $pdefaultgroupcolumn_temp
+#end if
+#if 'X' in str($pdefaultgroupcolumn):
+  #set $pdefaultgroupcolumn_temp = $pdefaultgroupcolumn.replace('X', '\\')
+  #set $pdefaultgroupcolumn = $pdefaultgroupcolumn_temp
+#end if
+#if '__sq__' in str($pdefaultgroupcolumn):
+  #set $pdefaultgroupcolumn_temp = $pdefaultgroupcolumn.replace('__sq__', "'")
+  #set $pdefaultgroupcolumn = $pdefaultgroupcolumn_temp
+#end if
+#if '__db__' in str($pdefaultgroupcolumn):
+  #set $pdefaultgroupcolumn_temp = $pdefaultgroupcolumn.replace('__db__', '"')
+  #set $pdefaultgroupcolumn = $pdefaultgroupcolumn_temp
+#end if
 
 #if str($pdefaultgroupcolumn):
- --p-default-group-column="$pdefaultgroupcolumn"
+  --p-default-group-column=$pdefaultgroupcolumn
 #end if
 
 #if str($pdefaultmetric):
- --p-default-metric="$pdefaultmetric"
-#end if
-
-#if str($pyscale) != 'None':
- --p-yscale=$pyscale
+  --p-default-metric=$pdefaultmetric
 #end if
-
-
-#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($input_files_mmetadatafile)
+#if str($pyscale) != 'None':
+--p-yscale=$pyscale
 #end if
 
-
 --o-visualization=ovisualization
+
+#if str($examples) != 'None':
+--examples=$examples
+#end if
+
 ;
-qiime tools export --input-path ovisualization.qzv --output-path out   && mkdir -p '$ovisualization.files_path'
+cp odistancematrix.qza $odistancematrix
+
+;
+qiime tools export  ovisualization.qzv --output-path out
+&& mkdir -p '$ovisualization.files_path'
+&& cp -r out/* '$ovisualization.files_path'
+&& mv '$ovisualization.files_path/index.html' '$ovisualization'
+
+;
+qiime tools export  ovisualization.qzv --output-path out
+&& mkdir -p '$ovisualization.files_path'
+&& cp -r out/* '$ovisualization.files_path'
+&& mv '$ovisualization.files_path/index.html' '$ovisualization'
+
+;
+qiime tools export  ovisualization.qzv --output-path out
+&& mkdir -p '$ovisualization.files_path'
+&& cp -r out/* '$ovisualization.files_path'
+&& mv '$ovisualization.files_path/index.html' '$ovisualization'
+
+;
+qiime tools export  ovisualization.qzv --output-path out
+&& mkdir -p '$ovisualization.files_path'
 && cp -r out/* '$ovisualization.files_path'
-&& mv '$ovisualization.files_path/index.html' '$ovisualization';
-	]]></command>
-	<inputs>
-		<param label="--p-state-column: TEXT  Metadata column containing state (time) variable information.                               [required]" name="pstatecolumn" optional="False" type="text"/>
-		<param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[RelativeFrequency] Feature table containing metrics.          [optional]" name="itable" optional="True" type="data"/>
-		<param label="--p-individual-id-column: TEXT Metadata column containing IDs for individual subjects.                                  [optional]" name="pindividualidcolumn" optional="True" type="text"/>
-		<param label="--p-default-group-column: TEXT The default metadata column on which to separate groups for comparison (all categorical metadata columns will be available in the visualization). [optional]" name="pdefaultgroupcolumn" optional="True" type="text"/>
-		<param label="--p-default-metric: TEXT Numeric metadata or artifact column to test by default (all numeric metadata columns will be available in the visualization).           [optional]" name="pdefaultmetric" optional="True" type="text"/>
-		<param label="--p-yscale: " name="pyscale" optional="True" type="select">
-			<option selected="True" value="None">Selection is Optional</option>
-			<option value="linear">linear</option>
-			<option value="pow">pow</option>
-			<option value="sqrt">sqrt</option>
-			<option value="log">log</option>
-		</param>
+&& mv '$ovisualization.files_path/index.html' '$ovisualization'
 
-		<repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file  [required]">
-			<param label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [optional]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
-		</repeat>
+  ]]></command>
+  <inputs>
+    <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[RelativeFrequency] Feature table containing metrics.          [optional]" name="itable" optional="False" type="data" />
+    <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file">
+      <param format="tabular,qza,no_unzip.zip" label="--m-metadata-file: METADATA... (multiple            Sample metadata file containing arguments will be   individual-id-column. merged)                                                        [required]" name="additional_input" optional="False" type="data" />
+    </repeat>
+    <param label="--p-state-column: TEXT  Metadata column containing state (time) variable information.                               [required]" name="pstatecolumn" optional="False" type="text" />
+    <param label="--p-individual-id-column: TEXT Metadata column containing IDs for individual subjects.                                  [optional]" name="pindividualidcolumn" optional="False" type="text" />
+    <param label="--p-default-group-column: TEXT The default metadata column on which to separate groups for comparison (all categorical metadata columns will be available in the visualization). [optional]" name="pdefaultgroupcolumn" optional="False" type="text" />
+    <param label="--p-default-metric: TEXT Numeric metadata or artifact column to test by default (all numeric metadata columns will be available in the visualization).           [optional]" name="pdefaultmetric" optional="False" type="text" />
+    <param label="--p-yscale: " name="pyscale" optional="True" type="select">
+      <option selected="True" value="None">Selection is Optional</option>
+      <option value="linear">linear</option>
+      <option value="pow">pow</option>
+      <option value="sqrt">sqrt</option>
+      <option value="log">log</option>
+    </param>
+    <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
+    
+  </inputs>
 
-	</inputs>
-	<outputs>
-		<data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
-	</outputs>
-	<help><![CDATA[
+  <outputs>
+    <data format="html" label="${tool.name} on ${on_string}: visualization.html" name="ovisualization" />
+    
+  </outputs>
+
+  <help><![CDATA[
 Generate interactive volatility plot
-####################################
+###############################################################
 
 Generate an interactive control chart depicting the longitudinal volatility
 of sample metadata and/or feature frequencies across time (as set using the
@@ -117,9 +200,9 @@
 Returns
 -------
 visualization : Visualization
-	]]></help>
-<macros>
+  ]]></help>
+  <macros>
     <import>qiime_citation.xml</import>
-</macros>
-<expand macro="qiime_citation"/>
-</tool>
+  </macros>
+  <expand macro="qiime_citation"/>
+</tool>
\ No newline at end of file