--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime_quality-control_evaluate-composition.xml	Thu May 24 02:11:44 2018 -0400
@@ -0,0 +1,205 @@
+<?xml version="1.0" ?>
+<tool id="qiime_quality-control_evaluate-composition" name="qiime quality-control evaluate-composition" version="2018.4">
+	<description> - Evaluate expected vs. observed taxonomic composition of samples</description>
+	<requirements>
+		<requirement type="package" version="2018.4">qiime2</requirement>
+	</requirements>
+	<command>
+	<![CDATA[
+	qiime quality-control evaluate-composition --i-expected-features=$iexpectedfeatures --i-observed-features=$iobservedfeatures
+
+	#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($input_files_mmetadatafile)
+	#end if
+
+	#if str($cmdconfig) != 'None':
+	 --cmd-config=$cmdconfig
+	#end if
+
+	#if $pplotrvalue:
+	  --p-plot-r-value
+	#else
+		--p-no-plot-r-value
+	#end if
+
+	#if str($mmetadatacolumn):
+	 --m-metadata-column="$mmetadatacolumn"
+	#end if
+
+	#if $pplotrsquared:
+	  --p-plot-r-squared
+	#else
+		--p-no-plot-r-squared
+	#end if
+
+	#if $pdepth:
+	 --p-depth=$pdepth
+	#end if
+
+	#if $pplottar:
+	  --p-plot-tar
+	#else
+		--p-no-plot-tar
+	#end if
+
+	#if $pplotobservedfeaturesratio:
+	  --p-plot-observed-features-ratio
+	#else
+		--p-no-plot-observed-features-ratio
+	#end if
+
+	#if str($ppalette) != 'None':
+	 --p-palette=$ppalette
+	#end if
+
+	#if $pplottdr:
+	  --p-plot-tdr
+	#else
+		--p-no-plot-tdr
+	#end if
+	 --o-visualization=ovisualization
+	#if $pplotobservedfeatures:
+	  --p-plot-observed-features
+	#else
+		--p-no-plot-observed-features
+	#end if
+	;
+	qiime tools export ovisualization.qzv --output-dir out   && mkdir -p '$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-expected-features: FeatureTable[RelativeFrequency] Expected feature compositions  [required]" name="iexpectedfeatures" optional="False" type="data"/>
+		<param format="qza,no_unzip.zip" label="--i-observed-features: FeatureTable[RelativeFrequency] Observed feature compositions  [required]" name="iobservedfeatures" optional="False" type="data"/>
+
+		<param label="--p-depth: Maximum depth of semicolon-delimited taxonomic ranks to test (e.g., 1 = root, 7 = species for the greengenes reference sequence database).  [default: 7]" name="pdepth" optional="True" type="integer" value="7"/>
+
+		<param label="--p-palette: Color palette to utilize for plotting.[default: Set1]" name="ppalette" optional="True" type="select">
+			<option selected="True" value="None">Selection is Optional</option>
+			<option value="Accent">Accent</option>
+			<option value="tab20">tab20</option>
+			<option value="Pastel2">Pastel2</option>
+			<option value="plasma">plasma</option>
+			<option value="viridis">viridis</option>
+			<option value="rainbow">rainbow</option>
+			<option value="Pastel1">Pastel1</option>
+			<option value="inferno">inferno</option>
+			<option value="magma">magma</option>
+			<option value="tab20b">tab20b</option>
+			<option value="Set3">Set3</option>
+			<option value="Set2">Set2</option>
+			<option value="Dark2">Dark2</option>
+			<option value="Set1">Set1</option>
+			<option value="tab10">tab10</option>
+			<option value="tab20c">tab20c</option>
+			<option value="terrain">terrain</option>
+			<option value="Paired">Paired</option>
+		</param>
+
+
+		<param label="--p-plot-tar / --p-no-plot-tar  Plot taxon accuracy rate (TAR) on score
+                                  plot. TAR is the number of true positive
+                                  features divided by the total number of
+                                  observed features (TAR = true positives 
+                                  (true positives + false positives)).
+                                  [default: True]" name="pplottar" checked="True" type="boolean"/>
+		<param label="--p-plot-tdr / --p-no-plot-tdr  Plot taxon detection rate (TDR) on score
+                                  plot. TDR is the number of true positive
+                                  features divided by the total number of
+                                  expected features (TDR = true positives 
+                                  (true positives + false negatives)).
+                                  [default: True]" name="pplottdr" checked="True" type="boolean"/>
+		<param label="--p-plot-r-value / --p-no-plot-r-value
+                                  Plot expected vs. observed linear regression
+                                  r value on score plot.  [default: False]" name="pplotrvalue" checked="False" type="boolean"/>
+		<param label="--p-plot-r-squared / --p-no-plot-r-squared
+                                  Plot expected vs. observed linear regression
+                                  r-squared value on score plot.  [default:
+                                  True]" name="pplotrsquared" checked="True" type="boolean"/>
+
+		<param label="--p-plot-observed-features / --p-no-plot-observed-features
+                                  Plot observed features count on score plot.
+                                  [default: False]" name="pplotobservedfeatures" checked="False" type="boolean"/>
+		<param label="--p-plot-observed-features-ratio / --p-no-plot-observed-features-ratio
+                                  Plot ratio of observed:expected features on
+                                  score plot.  [default: True]" name="pplotobservedfeaturesratio" checked="True" type="boolean"/>
+
+		<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>
+		<param label="--m-metadata-column: MetadataColumn[Categorical] Column from metadata file or artifact viewable as metadata. Optional sample metadata that maps observed_features sample IDs to expected_features sample IDs. [optional]" name="mmetadatacolumn" optional="True" type="text"/>
+
+		<param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
+	</inputs>
+	<outputs>
+		<data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
+	</outputs>
+	<help>
+		<![CDATA[
+Evaluate expected vs. observed taxonomic composition of samples
+----------------------------------------------------------------
+
+This visualizer compares the feature composition of pairs of observed and
+expected samples containing the same sample ID in two separate feature
+tables. Typically, feature composition will consist of taxonomy
+classifications or other semicolon-delimited feature annotations. Taxon
+accuracy rate, taxon detection rate, and linear regression scores between
+expected and observed observations are calculated at each semicolon-
+delimited rank, and plots of per-level accuracy and observation
+correlations are plotted. A histogram of distance between false positive
+observations and the nearest expected feature is also generated, where
+distance equals the number of rank differences between the observed feature
+and the nearest common lineage in the expected feature. This visualizer is
+most suitable for testing per-run data quality on sequencing runs that
+contain mock communities or other samples with known composition. Also
+suitable for sanity checks of bioinformatics pipeline performance.
+
+Parameters
+----------
+expected_features : FeatureTable[RelativeFrequency]
+    Expected feature compositions
+observed_features : FeatureTable[RelativeFrequency]
+    Observed feature compositions
+depth : Int, optional
+    Maximum depth of semicolon-delimited taxonomic ranks to test (e.g., 1 =
+    root, 7 = species for the greengenes reference sequence database).
+palette : Str % Choices({'Accent', 'Dark2', 'Paired', 'Pastel1', 'Pastel2', 'Set1', 'Set2', 'Set3', 'inferno', 'magma', 'plasma', 'rainbow', 'tab10', 'tab20', 'tab20b', 'tab20c', 'terrain', 'viridis'}), optional
+    Color palette to utilize for plotting.
+plot_tar : Bool, optional
+    Plot taxon accuracy rate (TAR) on score plot. TAR is the number of true
+    positive features divided by the total number of observed features (TAR
+    = true positives / (true positives + false positives)).
+plot_tdr : Bool, optional
+    Plot taxon detection rate (TDR) on score plot. TDR is the number of
+    true positive features divided by the total number of expected features
+    (TDR = true positives / (true positives + false negatives)).
+plot_r_value : Bool, optional
+    Plot expected vs. observed linear regression r value on score plot.
+plot_r_squared : Bool, optional
+    Plot expected vs. observed linear regression r-squared value on score
+    plot.
+plot_observed_features : Bool, optional
+    Plot observed features count on score plot.
+plot_observed_features_ratio : Bool, optional
+    Plot ratio of observed:expected features on score plot.
+metadata : MetadataColumn[Categorical], optional
+    Optional sample metadata that maps observed_features sample IDs to
+    expected_features sample IDs.
+
+Returns
+-------
+visualization : Visualization
+		\
+		]]>
+	</help>
+</tool>