annotate qiime2/qiime_diversity_beta-correlation.xml @ 10:21c7954105a9 draft

Fix

<?xml version="1.0" ?>
<tool id="qiime_diversity_beta-correlation" name="qiime diversity beta-correlation" version="2019.7">
	<description> - Beta diversity correlation</description>
	<requirements>
		<requirement type="package" version="2019.7">qiime2</requirement>
	</requirements>
	<command><![CDATA[
qiime diversity beta-correlation

--i-distance-matrix=$idistancematrix



#if '__sq__' in str($mmetadatacolumn):
  #set $mmetadatacolumn_temp = $mmetadatacolumn.replace('__sq__', "'")
  #set $mmetadatacolumn = $mmetadatacolumn_temp
#end if

--m-metadata-column="$mmetadatacolumn"



#if str($pmethod) != 'None':
 --p-method=$pmethod
#end if

#if str($ppermutations):
 --p-permutations=$ppermutations
#end if

#if str($pintersectids):
 --p-intersect-ids
#end if




#if '__sq__' in str($plabel1):
  #set $plabel1_temp = $plabel1.replace('__sq__', "'")
  #set $plabel1 = $plabel1_temp
#end if

#if str($plabel1):
 --p-label1="$plabel1"
#end if



#if '__sq__' in str($plabel2):
  #set $plabel2_temp = $plabel2.replace('__sq__', "'")
  #set $plabel2 = $plabel2_temp
#end if

#if str($plabel2):
 --p-label2="$plabel2"
#end if



#if $metadatafile:
 --m-metadata-file=$metadatafile
#end if




--o-metadata-distance-matrix=ometadatadistancematrix
--o-mantel-scatter-visualization=omantelscattervisualization
;
cp ometadatadistancematrix.qza $ometadatadistancematrix;
qiime tools export --input-path omantelscattervisualization.qzv --output-path out   && mkdir -p '$omantelscattervisualization.files_path'
&& cp -r out/* '$omantelscattervisualization.files_path'
&& mv '$omantelscattervisualization.files_path/index.html' '$omantelscattervisualization'
	]]></command>
	<inputs>
		<param format="qza,no_unzip.zip" label="--i-distance-matrix: ARTIFACT DistanceMatrix     Matrix of distances between pairs of samples. [required]" name="idistancematrix" optional="False" type="data"/>
		<param label="--m-metadata-column: COLUMN  MetadataColumn[Numeric] Numeric metadata column from which to compute pairwise Euclidean distances                          [required]" name="mmetadatacolumn" optional="False" type="text"/>
		<param label="--p-method: " name="pmethod" optional="True" type="select">
			<option selected="True" value="None">Selection is Optional</option>
			<option value="spearman">spearman</option>
			<option value="pearson">pearson</option>
		</param>
		<param label="--p-permutations: INTEGER Range(0, None)     The number of permutations to be run when computing p-values. Supplying a value of zero will disable permutation testing and p-values will not be calculated (this results in *much* quicker execution time if p-values are not desired).               [default: 999]" name="ppermutations" optional="True" type="integer" min="0" value="999"/>
		<param label="--p-intersect-ids: --p-no-intersect-ids If supplied, IDs that are not found in both distance matrices will be discarded before applying the Mantel test. Default behavior is to error on any mismatched IDs.                                   [default: False]" name="pintersectids" selected="False" type="boolean"/>
		<param label="--p-label1: TEXT      Label for `distance-matrix` in the output visualization.                    [default: 'Metadata']" name="plabel1" optional="True" type="text" value="Metadata"/>
		<param label="--p-label2: TEXT      Label for `metadata-distance-matrix` in the output visualization.             [default: 'Distance Matrix']" name="plabel2" optional="True" type="text" value="Distance Matrix"/>

		<param label="--m-metadata-file METADATA" name="metadatafile" type="data" format="tabular,qza,no_unzip.zip" optional="True" />

	</inputs>
	<outputs>
		<data format="qza" label="${tool.name} on ${on_string}: metadatadistancematrix.qza" name="ometadatadistancematrix"/>
		<data format="html" label="${tool.name} on ${on_string}: mantelscattervisualization.qzv" name="omantelscattervisualization"/>
	</outputs>
	<help><![CDATA[
Beta diversity correlation
##########################

Create a distance matrix from a numeric metadata column and apply a two-
sided Mantel test to identify correlation between two distance matrices.
Actions used internally: `distance-matrix` from q2-metadata and `mantel`
from q2-diversity.

Parameters
----------
metadata : MetadataColumn[Numeric]
    Numeric metadata column from which to compute pairwise Euclidean
    distances
distance_matrix : DistanceMatrix
    Matrix of distances between pairs of samples.
method : Str % Choices('spearman', 'pearson'), optional
    The correlation test to be applied in the Mantel test.
permutations : Int % Range(0, None), optional
    The number of permutations to be run when computing p-values. Supplying
    a value of zero will disable permutation testing and p-values will not
    be calculated (this results in *much* quicker execution time if
    p-values are not desired).
intersect_ids : Bool, optional
    If supplied, IDs that are not found in both distance matrices will be
    discarded before applying the Mantel test. Default behavior is to error
    on any mismatched IDs.
label1 : Str, optional
    Label for `distance_matrix` in the output visualization.
label2 : Str, optional
    Label for `metadata_distance_matrix` in the output visualization.

Returns
-------
metadata_distance_matrix : DistanceMatrix
    The Distance Matrix produced from the metadata column and used in the
    mantel test
mantel_scatter_visualization : Visualization
    Scatter plot rendering of the manteltest results
	]]></help>
<macros>
    <import>qiime_citation.xml</import>
</macros>
<expand macro="qiime_citation"/>
</tool>