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diff qiime2/qiime_gneiss_dendrogram-heatmap.xml @ 14:a0a8d77a991c draft

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author florianbegusch
date Thu, 03 Sep 2020 09:51:29 +0000
parents f190567fe3f6
children
line wrap: on
line diff
--- a/qiime2/qiime_gneiss_dendrogram-heatmap.xml	Thu Sep 03 09:46:00 2020 +0000
+++ b/qiime2/qiime_gneiss_dendrogram-heatmap.xml	Thu Sep 03 09:51:29 2020 +0000
@@ -1,152 +1,187 @@
 <?xml version="1.0" ?>
-<tool id="qiime_gneiss_dendrogram-heatmap" name="qiime gneiss dendrogram-heatmap" version="2019.7">
-	<description> - Dendrogram heatmap.</description>
-	<requirements>
-		<requirement type="package" version="2019.7">qiime2</requirement>
-	</requirements>
-	<command><![CDATA[
+<tool id="qiime_gneiss_dendrogram-heatmap" name="qiime gneiss dendrogram-heatmap"
+      version="2020.8">
+  <description>Dendrogram heatmap.</description>
+  <requirements>
+    <requirement type="package" version="2020.8">qiime2</requirement>
+  </requirements>
+  <command><![CDATA[
 qiime gneiss dendrogram-heatmap
 
 --i-table=$itable
+
 --i-tree=$itree
---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($input_files_mmetadatafile)
+# end if
+
+#if '__ob__' in str($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 $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($input_files_mmetadatafile)
-#end if
+--p-pseudocount=$ppseudocount
 
-
-#if str($ppseudocount):
- --p-pseudocount=$ppseudocount
-#end if
-
-#if str($pndim):
- --p-ndim=$pndim
-#end if
+--p-ndim=$pndim
 
 #if str($pmethod) != 'None':
- --p-method=$pmethod
+--p-method=$pmethod
 #end if
 
 #if str($pcolormap) != 'None':
- --p-color-map=$pcolormap
+--p-color-map=$pcolormap
 #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 oclustering.qza $oclustering
+
+;
+qiime tools export  ovisualization.qzv --output-path out
+&& mkdir -p '$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[Frequency] The feature table that will be plotted as a heatmap. This table is assumed to have strictly positive values.                          [required]" name="itable" optional="False" type="data"/>
-		<param format="qza,no_unzip.zip" label="--i-tree: ARTIFACT       A hierarchy of feature identifiers where each Hierarchy             tipcorresponds to the feature identifiers in the table. This tree can contain tip ids that are not present in the table, but all feature ids in the table must be present in this tree.       [required]" name="itree" optional="False" type="data"/>
-		<param label="--m-metadata-column: COLUMN  MetadataColumn[Categorical] Categorical metadata column to group the samples. [required]" name="mmetadatacolumn" optional="False" type="text"/>
-		<param label="--p-pseudocount: NUMBER  The pseudocount to add to avoid division by zero. [default: 0.5]" name="ppseudocount" optional="True" type="float" value="0.5"/>
-		<param label="--p-ndim: INTEGER        Number of dimensions to highlight.     [default: 10]" name="pndim" optional="True" type="integer" value="10"/>
-		<param label="--p-method: " name="pmethod" optional="True" type="select">
-			<option selected="True" value="None">Selection is Optional</option>
-			<option value="clr">clr</option>
-			<option value="log">log</option>
-		</param>
-		<param label="--p-color-map: " name="pcolormap" optional="True" type="select">
-			<option selected="True" value="None">Selection is Optional</option>
-			<option value="viridis">viridis</option>
-			<option value="inferno">inferno</option>
-			<option value="plasma">plasma</option>
-			<option value="magma">magma</option>
-			<option value="Blues">Blues</option>
-			<option value="BuGn">BuGn</option>
-			<option value="BuPu">BuPu</option>
-			<option value="GnBu">GnBu</option>
-			<option value="Greens">Greens</option>
-			<option value="Greys">Greys</option>
-			<option value="Oranges">Oranges</option>
-			<option value="OrRd">OrRd</option>
-			<option value="PuBu">PuBu</option>
-			<option value="PuBuGn">PuBuGn</option>
-			<option value="PuRd">PuRd</option>
-			<option value="Purples">Purples</option>
-			<option value="RdPu">RdPu</option>
-			<option value="Reds">Reds</option>
-			<option value="YlGn">YlGn</option>
-			<option value="YlGnBu">YlGnBu</option>
-			<option value="YlOrBr">YlOrBr</option>
-			<option value="YlOrRd">YlOrRd</option>
-			<option value="afmhot">afmhot</option>
-			<option value="autumn">autumn</option>
-			<option value="bone">bone</option>
-			<option value="cool">cool</option>
-			<option value="copper">copper</option>
-			<option value="gist_heat">gist_heat</option>
-			<option value="gray">gray</option>
-			<option value="hot">hot</option>
-			<option value="pink">pink</option>
-			<option value="spring">spring</option>
-			<option value="summer">summer</option>
-			<option value="winter">winter</option>
-			<option value="BrBG">BrBG</option>
-			<option value="bwr">bwr</option>
-			<option value="coolwarm">coolwarm</option>
-			<option value="PiYG">PiYG</option>
-			<option value="PRGn">PRGn</option>
-			<option value="PuOr">PuOr</option>
-			<option value="RdBu">RdBu</option>
-			<option value="RdGy">RdGy</option>
-			<option value="RdYlBu">RdYlBu</option>
-			<option value="RdYlGn">RdYlGn</option>
-			<option value="Spectral">Spectral</option>
-			<option value="seismic">seismic</option>
-			<option value="Accent">Accent</option>
-			<option value="Dark2">Dark2</option>
-			<option value="Paired">Paired</option>
-			<option value="Pastel1">Pastel1</option>
-			<option value="Pastel2">Pastel2</option>
-			<option value="Set1">Set1</option>
-			<option value="Set2">Set2</option>
-			<option value="Set3">Set3</option>
-			<option value="Vega10">Vega10</option>
-			<option value="Vega20">Vega20</option>
-			<option value="Vega20b">Vega20b</option>
-			<option value="Vega20c">Vega20c</option>
-			<option value="gist_earth">gist_earth</option>
-			<option value="terrain">terrain</option>
-			<option value="ocean">ocean</option>
-			<option value="gist_stern">gist_stern</option>
-			<option value="brg">brg</option>
-			<option value="CMRmap">CMRmap</option>
-			<option value="cubehelix">cubehelix</option>
-			<option value="gnuplot">gnuplot</option>
-			<option value="gnuplot2">gnuplot2</option>
-			<option value="gist_ncar">gist_ncar</option>
-			<option value="nipy_spectral">nipy_spectral</option>
-			<option value="jet">jet</option>
-			<option value="rainbow">rainbow</option>
-			<option value="gist_rainbow">gist_rainbow</option>
-			<option value="hsv">hsv</option>
-			<option value="flag">flag</option>
-			<option value="prism">prism</option>
-		</param>
 
-		<repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file">
-			<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[Frequency] The feature table that will be plotted as a heatmap. This table is assumed to have strictly positive values.                          [required]" name="itable" optional="False" type="data" />
+    <param format="qza,no_unzip.zip" label="--i-tree: ARTIFACT       A hierarchy of feature identifiers where each Hierarchy             tipcorresponds to the feature identifiers in the table. This tree can contain tip ids that are not present in the table, but all feature ids in the table must be present in this tree.       [required]" name="itree" 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 metadata column to group the samples. [required]" name="mmetadatacolumn" optional="False" type="text" />
+    <param label="--p-pseudocount: NUMBER  The pseudocount to add to avoid division by zero. [default: 0.5]" name="ppseudocount" optional="True" type="float" value="0.5" />
+    <param label="--p-ndim: INTEGER        Number of dimensions to highlight.     [default: 10]" name="pndim" optional="True" type="integer" value="10" />
+    <param label="--p-method: " name="pmethod" optional="True" type="select">
+      <option selected="True" value="None">Selection is Optional</option>
+      <option value="clr">clr</option>
+      <option value="log">log</option>
+    </param>
+    <param label="--p-color-map: " name="pcolormap" optional="True" type="select">
+      <option selected="True" value="None">Selection is Optional</option>
+      <option value="viridis">viridis</option>
+      <option value="inferno">inferno</option>
+      <option value="plasma">plasma</option>
+      <option value="magma">magma</option>
+      <option value="Blues">Blues</option>
+      <option value="BuGn">BuGn</option>
+      <option value="BuPu">BuPu</option>
+      <option value="GnBu">GnBu</option>
+      <option value="Greens">Greens</option>
+      <option value="Greys">Greys</option>
+      <option value="Oranges">Oranges</option>
+      <option value="OrRd">OrRd</option>
+      <option value="PuBu">PuBu</option>
+      <option value="PuBuGn">PuBuGn</option>
+      <option value="PuRd">PuRd</option>
+      <option value="Purples">Purples</option>
+      <option value="RdPu">RdPu</option>
+      <option value="Reds">Reds</option>
+      <option value="YlGn">YlGn</option>
+      <option value="YlGnBu">YlGnBu</option>
+      <option value="YlOrBr">YlOrBr</option>
+      <option value="YlOrRd">YlOrRd</option>
+      <option value="afmhot">afmhot</option>
+      <option value="autumn">autumn</option>
+      <option value="bone">bone</option>
+      <option value="cool">cool</option>
+      <option value="copper">copper</option>
+      <option value="gist_heat">gist_heat</option>
+      <option value="gray">gray</option>
+      <option value="hot">hot</option>
+      <option value="pink">pink</option>
+      <option value="spring">spring</option>
+      <option value="summer">summer</option>
+      <option value="winter">winter</option>
+      <option value="BrBG">BrBG</option>
+      <option value="bwr">bwr</option>
+      <option value="coolwarm">coolwarm</option>
+      <option value="PiYG">PiYG</option>
+      <option value="PRGn">PRGn</option>
+      <option value="PuOr">PuOr</option>
+      <option value="RdBu">RdBu</option>
+      <option value="RdGy">RdGy</option>
+      <option value="RdYlBu">RdYlBu</option>
+      <option value="RdYlGn">RdYlGn</option>
+      <option value="Spectral">Spectral</option>
+      <option value="seismic">seismic</option>
+      <option value="Accent">Accent</option>
+      <option value="Dark2">Dark2</option>
+      <option value="Paired">Paired</option>
+      <option value="Pastel1">Pastel1</option>
+      <option value="Pastel2">Pastel2</option>
+      <option value="Set1">Set1</option>
+      <option value="Set2">Set2</option>
+      <option value="Set3">Set3</option>
+      <option value="Vega10">Vega10</option>
+      <option value="Vega20">Vega20</option>
+      <option value="Vega20b">Vega20b</option>
+      <option value="Vega20c">Vega20c</option>
+      <option value="gist_earth">gist_earth</option>
+      <option value="terrain">terrain</option>
+      <option value="ocean">ocean</option>
+      <option value="gist_stern">gist_stern</option>
+      <option value="brg">brg</option>
+      <option value="CMRmap">CMRmap</option>
+      <option value="cubehelix">cubehelix</option>
+      <option value="gnuplot">gnuplot</option>
+      <option value="gnuplot2">gnuplot2</option>
+      <option value="gist_ncar">gist_ncar</option>
+      <option value="nipy_spectral">nipy_spectral</option>
+      <option value="jet">jet</option>
+      <option value="rainbow">rainbow</option>
+      <option value="gist_rainbow">gist_rainbow</option>
+      <option value="hsv">hsv</option>
+      <option value="flag">flag</option>
+      <option value="prism">prism</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[
 Dendrogram heatmap.
-###################
+###############################################################
+
+.. deprecated::
+   This Visualizer is deprecated and will be removed in a future version of
+   this plugin.
 
 Visualize the feature table as a heatmap, with samples sorted along a
 specified categorical metadata column and features clustered together
@@ -179,9 +214,9 @@
 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