diff qiime2/qiime_demux_filter-samples.xml @ 29:3ba9833030c1 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_demux_filter-samples.xml	Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,113 @@
+<?xml version="1.0" ?>
+<tool id="qiime_demux_filter-samples" name="qiime demux filter-samples"
+      version="2020.8">
+  <description>Filter samples out of demultiplexed data.</description>
+  <requirements>
+    <requirement type="package" version="2020.8">qiime2</requirement>
+  </requirements>
+  <command><![CDATA[
+qiime demux filter-samples
+
+--i-demux=$idemux
+# 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 $pexcludeids:
+ --p-exclude-ids
+#end if
+
+--o-filtered-demux=ofiltereddemux
+
+#if str($examples) != 'None':
+--examples=$examples
+#end if
+
+;
+cp ofiltereddemux.qza $ofiltereddemux
+
+  ]]></command>
+  <inputs>
+    <param format="qza,no_unzip.zip" label="--i-demux: ARTIFACT SampleData[SequencesWithQuality¹ | PairedEndSequencesWithQuality² | JoinedSequencesWithQuality³] The demultiplexed data from which samples should be filtered.                                    [required]" name="idemux" optional="False" type="data" />
+    <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file">
+      <param format="tabular,qza,no_unzip.zip" label="--m-metadata-file: METADATA... (multiple          Sample metadata indicating which sample ids to filter. arguments will    The optional `where` parameter may be used to filter be merged)        ids based on specified conditions in the metadata. The optional `exclude-ids` parameter may be used to exclude the ids specified in the metadata from the filter. [required]" name="additional_input" optional="False" type="data" />
+    </repeat>
+    <param label="--p-where: TEXT       Optional SQLite WHERE clause specifying sample metadata criteria that must be met to be included in the filtered data. If not provided, all samples in `metadata` that are also in the demultiplexed data will be retained.                                 [optional]" name="pwhere" optional="False" type="text" />
+    <param label="--p-exclude-ids: --p-exclude-ids: / --p-no-exclude-ids Defaults to False. If True, the samples selected by the `metadata` and optional `where` parameter will be excluded from the filtered data.       [default: False]" name="pexcludeids" selected="False" type="boolean" />
+    <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
+    
+  </inputs>
+
+  <outputs>
+    <data format="qza" label="${tool.name} on ${on_string}: filtereddemux.qza" name="ofiltereddemux" />
+    
+  </outputs>
+
+  <help><![CDATA[
+Filter samples out of demultiplexed data.
+###############################################################
+
+Filter samples indicated in given metadata out of demultiplexed data.
+Specific samples can be further selected with the WHERE clause, and the
+`exclude_ids` parameter allows for filtering of all samples not specified.
+
+Parameters
+----------
+demux : SampleData[SequencesWithQuality¹ | PairedEndSequencesWithQuality² | JoinedSequencesWithQuality³]
+    The demultiplexed data from which samples should be filtered.
+metadata : Metadata
+    Sample metadata indicating which sample ids to filter. The optional
+    `where` parameter may be used to filter ids based on specified
+    conditions in the metadata. The optional `exclude_ids` parameter may be
+    used to exclude the ids specified in the metadata from the filter.
+where : Str, optional
+    Optional SQLite WHERE clause specifying sample metadata criteria that
+    must be met to be included in the filtered data. If not provided, all
+    samples in `metadata` that are also in the demultiplexed data will be
+    retained.
+exclude_ids : Bool, optional
+    Defaults to False. If True, the samples selected by the `metadata` and
+    optional `where` parameter will be excluded from the filtered data.
+
+Returns
+-------
+filtered_demux : SampleData[SequencesWithQuality¹ | PairedEndSequencesWithQuality² | JoinedSequencesWithQuality³]
+    Filtered demultiplexed data.
+  ]]></help>
+  <macros>
+    <import>qiime_citation.xml</import>
+  </macros>
+  <expand macro="qiime_citation"/>
+</tool>
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