diff qiime2-2020.8/qiime_longitudinal_nmit.xml @ 20:d93d8888f0b0 draft

Uploaded

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+++ b/qiime2-2020.8/qiime_longitudinal_nmit.xml	Fri Sep 04 12:44:24 2020 +0000
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+<?xml version="1.0" ?>
+<tool id="qiime_longitudinal_nmit" name="qiime longitudinal nmit"
+      version="2020.8">
+  <description>Nonparametric microbial interdependence test</description>
+  <requirements>
+    <requirement type="package" version="2020.8">qiime2</requirement>
+  </requirements>
+  <command><![CDATA[
+qiime longitudinal nmit
+
+--i-table=$itable
+# 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($input_files_mmetadatafile)
+# end if
+
+#if '__ob__' in str($pindividualidcolumn):
+  #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('__ob__', '[')
+  #set $pindividualidcolumn = $pindividualidcolumn_temp
+#end if
+#if '__cb__' in str($pindividualidcolumn):
+  #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('__cb__', ']')
+  #set $pindividualidcolumn = $pindividualidcolumn_temp
+#end if
+#if 'X' in str($pindividualidcolumn):
+  #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('X', '\\')
+  #set $pindividualidcolumn = $pindividualidcolumn_temp
+#end if
+#if '__sq__' in str($pindividualidcolumn):
+  #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('__sq__', "'")
+  #set $pindividualidcolumn = $pindividualidcolumn_temp
+#end if
+#if '__db__' in str($pindividualidcolumn):
+  #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('__db__', '"')
+  #set $pindividualidcolumn = $pindividualidcolumn_temp
+#end if
+
+--p-individual-id-column=$pindividualidcolumn
+
+
+#if str($pcorrmethod) != 'None':
+--p-corr-method=$pcorrmethod
+#end if
+
+#if str($pdistmethod) != 'None':
+--p-dist-method=$pdistmethod
+#end if
+
+--o-distance-matrix=odistancematrix
+
+#if str($examples) != 'None':
+--examples=$examples
+#end if
+
+;
+cp odistancematrix.qza $odistancematrix
+
+  ]]></command>
+  <inputs>
+    <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[RelativeFrequency] Feature table to use for microbial interdependence test.                                       [required]" name="itable" optional="False" type="data" />
+    <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file">
+      <param format="tabular,qza,no_unzip.zip" label="--m-metadata-file: METADATA... (multiple           Sample metadata file containing individual-id-column. arguments will be merged)                                                        [required]" name="additional_input" optional="False" type="data" />
+    </repeat>
+    <param label="--p-individual-id-column: TEXT Metadata column containing IDs for individual subjects.                                   [required]" name="pindividualidcolumn" optional="False" type="text" />
+    <param label="--p-corr-method: " name="pcorrmethod" optional="True" type="select">
+      <option selected="True" value="None">Selection is Optional</option>
+      <option value="kendall">kendall</option>
+      <option value="pearson">pearson</option>
+      <option value="spearman">spearman</option>
+    </param>
+    <param label="--p-dist-method: " name="pdistmethod" optional="True" type="select">
+      <option selected="True" value="None">Selection is Optional</option>
+      <option value="fro">fro</option>
+      <option value="nuc">nuc</option>
+    </param>
+    <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
+    
+  </inputs>
+
+  <outputs>
+    <data format="qza" label="${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>
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