diff qiime2/qiime_quality-control_evaluate-composition.xml @ 0:370e0b6e9826 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_quality-control_evaluate-composition.xml	Wed Jul 17 03:05:17 2019 -0400
@@ -0,0 +1,182 @@
+<?xml version="1.0" ?>
+<tool id="qiime_quality-control_evaluate-composition" name="qiime quality-control evaluate-composition" version="2019.4">
+	<description> - Evaluate expected vs. observed taxonomic composition of samples</description>
+	<requirements>
+		<requirement type="package" version="2019.4">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 $pdepth:
+ --p-depth=$pdepth
+#end if
+
+#if str($ppalette) != 'None':
+ --p-palette=$ppalette
+#end if
+
+#if $pplottar:
+ --p-plot-tar
+#end if
+
+#if $pplottdr:
+ --p-plot-tdr
+#end if
+
+#if $pplotrvalue:
+ --p-plot-r-value
+#end if
+
+#if $pnoplotrsquared:
+ --p-no-plot-r-squared
+#end if
+
+#if $pplotbraycurtis:
+ --p-plot-bray-curtis
+#end if
+
+#if $pplotjaccard:
+ --p-plot-jaccard
+#end if
+
+#if $pplotobservedfeatures:
+ --p-plot-observed-features
+#end if
+
+#if $pplotobservedfeaturesratio:
+ --p-plot-observed-features-ratio
+#end if
+
+#if str($mmetadatacolumn):
+ --m-metadata-column="$mmetadatacolumn"
+#end if
+
+--o-visualization=ovisualization
+;
+qiime tools export --input-path ovisualization.qzv --output-path out   && mkdir -p '$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-expected-features: ARTIFACT FeatureTable[RelativeFrequency] Expected feature compositions                [required]" name="iexpectedfeatures" optional="False" type="data"/>
+		<param format="qza,no_unzip.zip" label="--i-observed-features: ARTIFACT FeatureTable[RelativeFrequency] Observed feature compositions                [required]" name="iobservedfeatures" optional="False" type="data"/>
+		<param label="--p-depth: INTEGER    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: " name="ppalette" optional="True" type="select">
+			<option selected="True" value="None">Selection is Optional</option>
+			<option value="Set1">Set1</option>
+			<option value="Set2">Set2</option>
+			<option value="Set3">Set3</option>
+			<option value="Pastel1">Pastel1</option>
+			<option value="Pastel2">Pastel2</option>
+			<option value="Paired">Paired</option>
+			<option value="Accent">Accent</option>
+			<option value="Dark2">Dark2</option>
+			<option value="tab10">tab10</option>
+			<option value="tab20">tab20</option>
+			<option value="tab20b">tab20b</option>
+			<option value="tab20c">tab20c</option>
+			<option value="viridis">viridis</option>
+			<option value="plasma">plasma</option>
+			<option value="inferno">inferno</option>
+			<option value="magma">magma</option>
+			<option value="terrain">terrain</option>
+			<option value="rainbow">rainbow</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 " name="pplottar" selected="False" 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 " name="pplottdr" selected="False" 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" selected="False" type="boolean"/>
+		<param label="--p-no-plot-r-squared: Do not plot expected vs. observed linear regression r-squared value on score plot.                    [default: False]" name="pnoplotrsquared" selected="False" type="boolean"/>
+		<param label="--p-plot-bray-curtis: --p-no-plot-bray-curtis Plot expected vs. observed Bray-Curtis dissimilarity scores on score plot.                  [default: False]" name="pplotbraycurtis" selected="False" type="boolean"/>
+		<param label="--p-plot-jaccard: --p-no-plot-jaccard Plot expected vs. observed Jaccard distances scores on score plot.                            [default: False]" name="pplotjaccard" selected="False" type="boolean"/>
+		<param label="--p-plot-observed-features: --p-no-plot-observed-features Plot observed features count on score plot. [default: False]" name="pplotobservedfeatures" selected="False" type="boolean"/>
+		<param label="--p-no-plot-observed-features-ratio: Do not plot ratio of observed:expected features on score plot.                                   [default: False]" name="pnoplotobservedfeaturesratio" selected="False" type="boolean"/>
+		<param label="--m-metadata-column: COLUMN  MetadataColumn[Categorical] Optional sample metadata that maps observed-features sample IDs to expected-features sample IDs.  [optional]" name="mmetadatacolumn" optional="True" type="text"/>
+
+		<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>
+
+	</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('Set1', 'Set2', 'Set3', 'Pastel1', 'Pastel2', 'Paired', 'Accent', 'Dark2', 'tab10', 'tab20', 'tab20b', 'tab20c', 'viridis', 'plasma', 'inferno', 'magma', 'terrain', 'rainbow'), 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_bray_curtis : Bool, optional
+    Plot expected vs. observed Bray-Curtis dissimilarity scores on score
+    plot.
+plot_jaccard : Bool, optional
+    Plot expected vs. observed Jaccard distances scores 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>
+<macros>
+    <import>qiime_citation.xml</import>
+</macros>
+<expand macro="qiime_citation"/>
+</tool>