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view qiime2/qiime_feature-table_filter-seqs.xml @ 29:3ba9833030c1 draft
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author | florianbegusch |
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date | Fri, 04 Sep 2020 13:12:49 +0000 |
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<?xml version="1.0" ?> <tool id="qiime_feature-table_filter-seqs" name="qiime feature-table filter-seqs" version="2020.8"> <description>Filter features from sequences</description> <requirements> <requirement type="package" version="2020.8">qiime2</requirement> </requirements> <command><![CDATA[ qiime feature-table filter-seqs # if $input_files_idata: # 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 + ' --i-data=' + d['additional_input'].__getattr__('file_name') # end for # return $file_list # end def --i-data=$list_dict_to_string($input_files_idata) # end if #if str($itable) != 'None': --i-table=$itable #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($input_files_mmetadatafile) # end if #if '__ob__' in str($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 $pexcludeids: --p-exclude-ids #end if --o-filtered-data=ofiltereddata #if str($examples) != 'None': --examples=$examples #end if ; cp ofiltereddata.qza $ofiltereddata ]]></command> <inputs> <repeat name="input_files_idata" optional="False" title="--i-data"> <param format="qza,no_unzip.zip" label="--i-data: ARTIFACT FeatureData[Sequence¹ | AlignedSequence²] The sequences from which features should be filtered. [required]" name="additional_input" optional="False" type="data" /> </repeat> <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] Table containing feature ids used for id-based filtering. [optional]" name="itable" optional="False" type="data" /> <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file"> <param format="tabular,qza,no_unzip.zip" label="--m-metadata-file: METADATA... (multiple Feature metadata used for id-based filtering, with arguments will `where` parameter when selecting features to retain, or be merged) with `exclude-ids` when selecting features to discard. [optional]" name="additional_input" optional="True" type="data" /> </repeat> <param label="--p-where: TEXT SQLite WHERE clause specifying feature metadata criteria that must be met to be included in the filtered feature table. If not provided, all features in `metadata` that are also in the sequences will be retained. [optional]" name="pwhere" optional="False" type="text" /> <param label="--p-exclude-ids: --p-exclude-ids: / --p-no-exclude-ids If true, the features selected by the `metadata` (with or without the `where` parameter) or `table` parameter will be excluded from the filtered sequences instead of being retained. [default: False]" name="pexcludeids" selected="False" type="boolean" /> <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" /> </inputs> <outputs> <data format="qza" label="${tool.name} on ${on_string}: filtereddata.qza" name="ofiltereddata" /> </outputs> <help><![CDATA[ Filter features from sequences ############################################################### Filter features from sequences based on a feature table or metadata. See the filtering tutorial on https://docs.qiime2.org for additional details. This method can filter based on ids in a table or a metadata file, but not both (i.e., the table and metadata options are mutually exclusive). Parameters ---------- data : FeatureData[Sequence¹ | AlignedSequence²] The sequences from which features should be filtered. table : FeatureTable[Frequency], optional Table containing feature ids used for id-based filtering. metadata : Metadata, optional Feature metadata used for id-based filtering, with `where` parameter when selecting features to retain, or with `exclude_ids` when selecting features to discard. where : Str, optional SQLite WHERE clause specifying feature metadata criteria that must be met to be included in the filtered feature table. If not provided, all features in `metadata` that are also in the sequences will be retained. exclude_ids : Bool, optional If true, the features selected by the `metadata` (with or without the `where` parameter) or `table` parameter will be excluded from the filtered sequences instead of being retained. Returns ------- filtered_data : FeatureData[Sequence¹ | AlignedSequence²] The resulting filtered sequences. ]]></help> <macros> <import>qiime_citation.xml</import> </macros> <expand macro="qiime_citation"/> </tool>