diff qiime2/qiime_gneiss_ols-regression.xml @ 0:370e0b6e9826 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_gneiss_ols-regression.xml	Wed Jul 17 03:05:17 2019 -0400
@@ -0,0 +1,80 @@
+<?xml version="1.0" ?>
+<tool id="qiime_gneiss_ols-regression" name="qiime gneiss ols-regression" version="2019.4">
+	<description> - Simplicial Ordinary Least Squares Regression</description>
+	<requirements>
+		<requirement type="package" version="2019.4">qiime2</requirement>
+	</requirements>
+	<command><![CDATA[
+qiime gneiss ols-regression
+
+--i-table=$itable
+--i-tree=$itree
+--p-formula="$pformula"
+
+
+#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($input_files_mmetadatafile)
+#end if
+
+
+--o-visualization=ovisualization
+;
+
+qiime tools export --input-path ovisualization.qzv --output-path out   && mkdir -p '$ovisualization.files_path'
+&& cp -r out/* '$ovisualization.files_path'
+&& mv '$ovisualization.files_path/index.html' '$ovisualization';
+	]]></command>
+	<inputs>
+		<param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Balance] The feature table containing the samples in which simplicial regression will be performed.     [required]" name="itable" optional="False" type="data"/>
+		<param format="qza,no_unzip.zip" label="--i-tree: ARTIFACT    A hierarchy of feature identifiers where each Hierarchy          tipcorresponds to the feature identifiers in the table. This tree can contain tip ids that are not present in the table, but all feature ids in the table must be present in this tree.                        [required]" name="itree" optional="False" type="data"/>
+		<param label="--p-formula: TEXT     Formula specifying the statistical model. In other words, a list of the metadata categories that will be used in the regression model, typically separated by '+'. For more information see https://patsy.readthedocs.io/en/latest/API-reference.html                                           [required]" name="pformula" optional="False" type="text"/>
+
+
+		<repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file">
+			<param label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [optional]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
+		</repeat>
+	</inputs>
+	<outputs>
+		<data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
+	</outputs>
+	<help><![CDATA[
+Simplicial Ordinary Least Squares Regression
+############################################
+
+Perform linear regression on balances. This will tell youhow much
+variability is explained by metadata categories in your formula.
+
+Parameters
+----------
+table : FeatureTable[Balance]
+    The feature table containing the samples in which simplicial regression
+    will be performed.
+tree : Hierarchy
+    A hierarchy of feature identifiers where each tipcorresponds to the
+    feature identifiers in the table. This tree can contain tip ids that
+    are not present in the table, but all feature ids in the table must be
+    present in this tree.
+metadata : Metadata
+    Metadata information that contains the covariates of interest.
+formula : Str
+    Formula specifying the statistical model. In other words, a list of the
+    metadata categories that will be used in the regression model,
+    typically separated by "+". For more information see
+    https://patsy.readthedocs.io/en/latest/API-reference.html
+
+Returns
+-------
+visualization : Visualization
+	]]></help>
+<macros>
+    <import>qiime_citation.xml</import>
+</macros>
+<expand macro="qiime_citation"/>
+</tool>