view qiime2/qiime_longitudinal_nmit.xml @ 5:a025a4a89e07 draft

Uploaded

<?xml version="1.0" ?>
<tool id="qiime_longitudinal_nmit" name="qiime longitudinal nmit" version="2019.4">
	<description> - Nonparametric microbial interdependence test</description>
	<requirements>
		<requirement type="package" version="2019.4">qiime2</requirement>
	</requirements>
	<command><![CDATA[
qiime longitudinal nmit

--i-table=$itable




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

#if str($pindividualidcolumn):
 --p-individual-id-column="$pindividualidcolumn"
#end if




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

#if str($pdistmethod) != 'None':
 --p-dist-method=$pdistmethod
#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


--o-distance-matrix=odistancematrix
;
cp odistancematrix.qza $odistancematrix
	]]></command>
	<inputs>
		<param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[RelativeFrequency] Feature table to use for microbial interdependence test.                                       [required]" name="itable" optional="False" type="data"/>
		<param label="--p-individual-id-column: TEXT Metadata column containing IDs for individual subjects.                                   [required]" name="pindividualidcolumn" optional="False" type="text"/>
		<param label="--p-corr-method: " name="pcorrmethod" optional="True" type="select">
			<option selected="True" value="None">Selection is Optional</option>
			<option value="kendall">kendall</option>
			<option value="pearson">pearson</option>
			<option value="spearman">spearman</option>
		</param>
		<param label="--p-dist-method: " name="pdistmethod" optional="True" type="select">
			<option selected="True" value="None">Selection is Optional</option>
			<option value="fro">fro</option>
			<option value="nuc">nuc</option>
		</param>

		<repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file  [required]">
			<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="qza" label="${tool.name} on ${on_string}: distancematrix.qza" name="odistancematrix"/>
	</outputs>
	<help><![CDATA[
Nonparametric microbial interdependence test
############################################

Perform nonparametric microbial interdependence test to determine
longitudinal sample similarity as a function of temporal microbial
composition. For more details and citation, please see
doi.org/10.1002/gepi.22065

Parameters
----------
table : FeatureTable[RelativeFrequency]
    Feature table to use for microbial interdependence test.
metadata : Metadata
    Sample metadata file containing individual_id_column.
individual_id_column : Str
    Metadata column containing IDs for individual subjects.
corr_method : Str % Choices('kendall', 'pearson', 'spearman'), optional
    The temporal correlation test to be applied.
dist_method : Str % Choices('fro', 'nuc'), optional
    Temporal distance method, see numpy.linalg.norm for details.

Returns
-------
distance_matrix : DistanceMatrix
    The resulting distance matrix.
	]]></help>
<macros>
    <import>qiime_citation.xml</import>
</macros>
<expand macro="qiime_citation"/>
</tool>