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author | florianbegusch |
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date | Fri, 04 Sep 2020 12:56:26 +0000 |
parents | d93d8888f0b0 |
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<?xml version="1.0" ?> <tool id="qiime_feature-table_filter-features" name="qiime feature-table filter-features" version="2020.8"> <description>Filter features from table</description> <requirements> <requirement type="package" version="2020.8">qiime2</requirement> </requirements> <command><![CDATA[ qiime feature-table filter-features --i-table=$itable --p-min-frequency=$pminfrequency #if str($pmaxfrequency): --p-max-frequency=$pmaxfrequency #end if --p-min-samples=$pminsamples #if str($pmaxsamples): --p-max-samples=$pmaxsamples #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 $pexcludeids: --p-exclude-ids #end if --o-filtered-table=ofilteredtable #if str($examples) != 'None': --examples=$examples #end if ; cp ofilteredtable.qza $ofilteredtable ]]></command> <inputs> <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] The feature table from which features should be filtered. [required]" name="itable" optional="False" type="data" /> <param label="--p-min-frequency: INTEGER The minimum total frequency that a feature must have to be retained. [default: 0]" name="pminfrequency" optional="True" type="integer" value="0" /> <param label="--p-max-frequency: INTEGER The maximum total frequency that a feature can have to be retained. If no value is provided this will default to infinity (i.e., no maximum frequency filter will be applied). [optional]" name="pmaxfrequency" optional="False" type="text" /> <param label="--p-min-samples: INTEGER The minimum number of samples that a feature must be observed in to be retained. [default: 0]" name="pminsamples" optional="True" type="integer" value="0" /> <param label="--p-max-samples: INTEGER The maximum number of samples that a feature can be observed in to be retained. If no value is provided this will default to infinity (i.e., no maximum sample filter will be applied). [optional]" name="pmaxsamples" optional="False" type="text" /> <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 with `where` parameter when arguments will selecting features to retain, or with `exclude-ids` be merged) 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 feature table 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 `metadata` or `where` parameters will be excluded from the filtered table 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}: filteredtable.qza" name="ofilteredtable" /> </outputs> <help><![CDATA[ Filter features from table ############################################################### Filter features from table based on frequency and/or metadata. Any samples with a frequency of zero after feature filtering will also be removed. See the filtering tutorial on https://docs.qiime2.org for additional details. Parameters ---------- table : FeatureTable[Frequency] The feature table from which features should be filtered. min_frequency : Int, optional The minimum total frequency that a feature must have to be retained. max_frequency : Int, optional The maximum total frequency that a feature can have to be retained. If no value is provided this will default to infinity (i.e., no maximum frequency filter will be applied). min_samples : Int, optional The minimum number of samples that a feature must be observed in to be retained. max_samples : Int, optional The maximum number of samples that a feature can be observed in to be retained. If no value is provided this will default to infinity (i.e., no maximum sample filter will be applied). metadata : Metadata, optional Feature metadata used 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 feature table will be retained. exclude_ids : Bool, optional If true, the features selected by `metadata` or `where` parameters will be excluded from the filtered table instead of being retained. Returns ------- filtered_table : FeatureTable[Frequency] The resulting feature table filtered by feature. ]]></help> <macros> <import>qiime_citation.xml</import> </macros> <expand macro="qiime_citation"/> </tool>