diff qiime2/qiime_longitudinal_volatility.xml @ 29:3ba9833030c1 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_longitudinal_volatility.xml	Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,208 @@
+<?xml version="1.0" ?>
+<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
+
+#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($input_files_mmetadatafile)
+# end if
+
+#if '__ob__' in str($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=$pindividualidcolumn
+#end if
+
+#if '__ob__' in str($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=$pdefaultgroupcolumn
+#end if
+
+#if str($pdefaultmetric):
+  --p-default-metric=$pdefaultmetric
+#end if
+#if str($pyscale) != 'None':
+--p-yscale=$pyscale
+#end if
+
+--o-visualization=ovisualization
+
+#if str($examples) != 'None':
+--examples=$examples
+#end if
+
+;
+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 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>
+
+  <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
+"state_column" parameter). Any numeric metadata column (and metadata-
+transformable artifacts, e.g., alpha diversity results) can be plotted on
+the y-axis, and are selectable using the "metric_column" selector. Metric
+values are averaged to compare across any categorical metadata column using
+the "group_column" selector. Longitudinal volatility for individual
+subjects sampled over time is co-plotted as "spaghetti" plots if the
+"individual_id_column" parameter is used. state_column will typically be a
+measure of time, but any numeric metadata column can be used.
+
+Parameters
+----------
+metadata : Metadata
+    Sample metadata file containing individual_id_column.
+state_column : Str
+    Metadata column containing state (time) variable information.
+individual_id_column : Str, optional
+    Metadata column containing IDs for individual subjects.
+default_group_column : Str, optional
+    The default metadata column on which to separate groups for comparison
+    (all categorical metadata columns will be available in the
+    visualization).
+default_metric : Str, optional
+    Numeric metadata or artifact column to test by default (all numeric
+    metadata columns will be available in the visualization).
+table : FeatureTable[RelativeFrequency], optional
+    Feature table containing metrics.
+yscale : Str % Choices('linear', 'pow', 'sqrt', 'log'), optional
+    y-axis scaling strategy to apply.
+
+Returns
+-------
+visualization : Visualization
+  ]]></help>
+  <macros>
+    <import>qiime_citation.xml</import>
+  </macros>
+  <expand macro="qiime_citation"/>
+</tool>
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