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author | florianbegusch |
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date | Fri, 04 Sep 2020 12:46:48 +0000 |
parents | d93d8888f0b0 |
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<?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>