Mercurial > repos > florianbegusch > qiime2_suite

diff qiime2/qiime_emperor_procrustes-plot.xml @ 14:a0a8d77a991c draft

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Uploaded
author florianbegusch
date Thu, 03 Sep 2020 09:51:29 +0000
parents f190567fe3f6
children
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line diff
--- a/qiime2/qiime_emperor_procrustes-plot.xml	Thu Sep 03 09:46:00 2020 +0000
+++ b/qiime2/qiime_emperor_procrustes-plot.xml	Thu Sep 03 09:51:29 2020 +0000
@@ -1,74 +1,82 @@
 <?xml version="1.0" ?>
-<tool id="qiime_emperor_procrustes-plot" name="qiime emperor procrustes-plot" version="2019.7">
-	<description> - Visualize and Interact with a procrustes plot</description>
-	<requirements>
-		<requirement type="package" version="2019.7">qiime2</requirement>
-	</requirements>
-	<command><![CDATA[
+<tool id="qiime_emperor_procrustes-plot" name="qiime emperor procrustes-plot"
+      version="2020.8">
+  <description>Visualize and Interact with a procrustes plot</description>
+  <requirements>
+    <requirement type="package" version="2020.8">qiime2</requirement>
+  </requirements>
+  <command><![CDATA[
 qiime emperor procrustes-plot
 
 --i-reference-pcoa=$ireferencepcoa
 
 --i-other-pcoa=$iotherpcoa
-
-
-#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($input_files_mmetadatafile)
-#end if
-
-
-
-#if '__sq__' in str($pcustomaxes):
-  #set $pcustomaxes_temp = $pcustomaxes.replace('__sq__', "'")
-  #set $pcustomaxes = $pcustomaxes_temp
-#end if
-
-#if '__cb__' in str($pcustomaxes):
-  #set $pcustomaxes_temp = $pcustomaxes.replace('__cb__', "]")
-  #set $pcustomaxes = $pcustomaxes_temp
-#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($pcustomaxes):
- --p-custom-axes="$pcustomaxes"
+  --p-custom-axes=$pcustomaxes
 #end if
-
-
-
-
 #if $pignoremissingsamples:
  --p-ignore-missing-samples
 #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' '$ovisualization'
-	]]></command>
-	<inputs>
-		<param format="qza,no_unzip.zip" label="--i-reference-pcoa: ARTIFACT PCoAResults        The reference ordination matrix to be plotted. [required]" name="ireferencepcoa" optional="False" type="data"/>
-		<param format="qza,no_unzip.zip" label="--i-other-pcoa: ARTIFACT PCoAResults        The 'other' ordination matrix to be plotted (the one that was fitted to the reference).           [required]" name="iotherpcoa" optional="False" type="data"/>
-		<param label="--p-custom-axes: TEXT... List[Str]          Numeric sample metadata columns that should be included as axes in the Emperor plot.        [optional]" name="pcustomaxes" optional="True" type="text"/>
-		<param label="--p-ignore-missing-samples: --p-no-ignore-missing-samples This will suppress the error raised when the coordinates matrix contains samples that are not present in the metadata. Samples without metadata are included by setting all metadata values to: 'This sample has no metadata'. This flag is only applied if at least one sample is present in both the coordinates matrix and the metadata.               [default: False]" name="pignoremissingsamples" selected="False" type="boolean"/>
+
+;
+qiime tools export  ovisualization.qzv --output-path out
+&& mkdir -p '$ovisualization.files_path'
+&& cp -r out/* '$ovisualization.files_path'
+&& mv '$ovisualization.files_path/index.html' '$ovisualization'
 
-		<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-reference-pcoa: ARTIFACT PCoAResults        The reference ordination matrix to be plotted. [required]" name="ireferencepcoa" optional="False" type="data" />
+    <param format="qza,no_unzip.zip" label="--i-other-pcoa: ARTIFACT PCoAResults        The \'other\' ordination matrix to be plotted (the one that was fitted to the reference).           [required]" name="iotherpcoa" 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          The sample metadata. arguments will be merged)                                                     [required]" name="additional_input" optional="False" type="data" />
+    </repeat>
+    <param label="--p-custom-axes: TEXT... List[Str]          Numeric sample metadata columns that should be included as axes in the Emperor plot.        [optional]" name="pcustomaxes" optional="False" type="text" />
+    <param label="--p-ignore-missing-samples: --p-ignore-missing-samples: / --p-no-ignore-missing-samples This will suppress the error raised when the coordinates matrix contains samples that are not present in the metadata. Samples without metadata are included by setting all metadata values to: \'This sample has no metadata\'. This flag is only applied if at least one sample is present in both the coordinates matrix and the metadata.               [default: False]" name="pignoremissingsamples" selected="False" type="boolean" />
+    <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[
 Visualize and Interact with a procrustes plot
-#############################################
+###############################################################
 
 Plot two procrustes-fitted matrices
 
@@ -94,9 +102,9 @@
 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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