diff qiime2-2020.8/qiime_quality-control_evaluate-composition.xml @ 20:d93d8888f0b0 draft

Uploaded

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+++ b/qiime2-2020.8/qiime_quality-control_evaluate-composition.xml	Fri Sep 04 12:44:24 2020 +0000
@@ -0,0 +1,214 @@
+<?xml version="1.0" ?>
+<tool id="qiime_quality-control_evaluate-composition" name="qiime quality-control evaluate-composition"
+      version="2020.8">
+  <description>Evaluate expected vs. observed taxonomic composition of samples</description>
+  <requirements>
+    <requirement type="package" version="2020.8">qiime2</requirement>
+  </requirements>
+  <command><![CDATA[
+qiime quality-control evaluate-composition
+
+--i-expected-features=$iexpectedfeatures
+
+--i-observed-features=$iobservedfeatures
+
+--p-depth=$pdepth
+
+#if str($ppalette) != 'None':
+--p-palette=$ppalette
+#end if
+
+#if $pnoplottar:
+ --p-no-plot-tar
+#end if
+
+#if $pnoplottdr:
+ --p-no-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 $pnoplotobservedfeaturesratio:
+ --p-no-plot-observed-features-ratio
+#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($input_files_mmetadatafile)
+# end if
+
+#if '__ob__' in str($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 = $mmetadatacolumn_temp
+#end if
+
+#if str($mmetadatacolumn):
+  --m-metadata-column=$mmetadatacolumn
+#end if
+
+--o-visualization=ovisualization
+
+#if str($examples) != 'None':
+--examples=$examples
+#end if
+
+;
+cp odatabase.qza $odatabase
+
+;
+qiime tools export  ovisualization.qzv --output-path out
+&& mkdir -p '$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-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-no-plot-tar: Do not 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="pnoplottar" selected="False" type="boolean" />
+    <param label="--p-no-plot-tdr: Do not 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="pnoplottdr" selected="False" type="boolean" />
+    <param label="--p-plot-r-value: --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: True]" name="pnoplotrsquared" selected="False" type="boolean" />
+    <param label="--p-plot-bray-curtis: --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-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-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: True]" name="pnoplotobservedfeaturesratio" selected="False" type="boolean" />
+    <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] Optional sample metadata that maps observed-features sample IDs to expected-features sample IDs.  [optional]" name="mmetadatacolumn" optional="False" type="text" />
+    <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[
+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>
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