diff qiime2-2020.8/qiime_diversity_filter-distance-matrix.xml @ 20:d93d8888f0b0 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2-2020.8/qiime_diversity_filter-distance-matrix.xml	Fri Sep 04 12:44:24 2020 +0000
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+<?xml version="1.0" ?>
+<tool id="qiime_diversity_filter-distance-matrix" name="qiime diversity filter-distance-matrix"
+      version="2020.8">
+  <description>Filter samples from a distance matrix.</description>
+  <requirements>
+    <requirement type="package" version="2020.8">qiime2</requirement>
+  </requirements>
+  <command><![CDATA[
+qiime diversity filter-distance-matrix
+
+--i-distance-matrix=$idistancematrix
+# 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($input_files_mmetadatafile)
+# end if
+
+#if '__ob__' in str($pwhere):
+  #set $pwhere_temp = $pwhere.replace('__ob__', '[')
+  #set $pwhere = $pwhere_temp
+#end if
+#if '__cb__' in str($pwhere):
+  #set $pwhere_temp = $pwhere.replace('__cb__', ']')
+  #set $pwhere = $pwhere_temp
+#end if
+#if 'X' in str($pwhere):
+  #set $pwhere_temp = $pwhere.replace('X', '\\')
+  #set $pwhere = $pwhere_temp
+#end if
+#if '__sq__' in str($pwhere):
+  #set $pwhere_temp = $pwhere.replace('__sq__', "'")
+  #set $pwhere = $pwhere_temp
+#end if
+#if '__db__' in str($pwhere):
+  #set $pwhere_temp = $pwhere.replace('__db__', '"')
+  #set $pwhere = $pwhere_temp
+#end if
+
+#if str($pwhere):
+  --p-where=$pwhere
+#end if
+
+#if $pexcludeids:
+ --p-exclude-ids
+#end if
+
+--o-filtered-distance-matrix=ofiltereddistancematrix
+
+#if str($examples) != 'None':
+--examples=$examples
+#end if
+
+;
+cp ofiltereddistancematrix.qza $ofiltereddistancematrix
+
+  ]]></command>
+  <inputs>
+    <param format="qza,no_unzip.zip" label="--i-distance-matrix: ARTIFACT DistanceMatrix     Distance matrix to filter by sample.         [required]" name="idistancematrix" optional="False" type="data" />
+    <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file">
+      <param format="tabular,qza,no_unzip.zip" label="--m-metadata-file: METADATA... (multiple          Sample metadata used with `where` parameter when arguments will    selecting samples to retain, or with `exclude-ids` when be merged)        selecting samples to discard.                [required]" name="additional_input" optional="False" type="data" />
+    </repeat>
+    <param label="--p-where: TEXT       SQLite WHERE clause specifying sample metadata criteria that must be met to be included in the filtered distance matrix. If not provided, all samples in `metadata` that are also in the input distance matrix will be retained.                     [optional]" name="pwhere" optional="False" type="text" />
+    <param label="--p-exclude-ids: --p-exclude-ids: / --p-no-exclude-ids If `True`, the samples selected by `metadata` or `where` parameters will be excluded from the filtered distance matrix instead of being retained. [default: False]" name="pexcludeids" selected="False" type="boolean" />
+    <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
+    
+  </inputs>
+
+  <outputs>
+    <data format="qza" label="${tool.name} on ${on_string}: filtereddistancematrix.qza" name="ofiltereddistancematrix" />
+    
+  </outputs>
+
+  <help><![CDATA[
+Filter samples from a distance matrix.
+###############################################################
+
+Filter samples from a distance matrix, retaining only the samples matching
+search criteria specified by `metadata` and `where` parameters (or
+retaining only the samples not matching that criteria, if `exclude_ids` is
+True). See the filtering tutorial on https://docs.qiime2.org for additional
+details.
+
+Parameters
+----------
+distance_matrix : DistanceMatrix
+    Distance matrix to filter by sample.
+metadata : Metadata
+    Sample metadata used with `where` parameter when selecting samples to
+    retain, or with `exclude_ids` when selecting samples to discard.
+where : Str, optional
+    SQLite WHERE clause specifying sample metadata criteria that must be
+    met to be included in the filtered distance matrix. If not provided,
+    all samples in `metadata` that are also in the input distance matrix
+    will be retained.
+exclude_ids : Bool, optional
+    If `True`, the samples selected by `metadata` or `where` parameters
+    will be excluded from the filtered distance matrix instead of being
+    retained.
+
+Returns
+-------
+filtered_distance_matrix : DistanceMatrix
+    Distance matrix filtered to include samples matching search criteria
+  ]]></help>
+  <macros>
+    <import>qiime_citation.xml</import>
+  </macros>
+  <expand macro="qiime_citation"/>
+</tool>
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