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view qiime2/qiime_feature-table_filter-samples.xml @ 8:d66c7509e8f9 draft
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author | florianbegusch |
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date | Tue, 13 Aug 2019 07:57:53 -0400 |
parents | a025a4a89e07 |
children | f190567fe3f6 |
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<?xml version="1.0" ?> <tool id="qiime_feature-table_filter-samples" name="qiime feature-table filter-samples" version="2019.4"> <description> - Filter samples from table</description> <requirements> <requirement type="package" version="2019.4">qiime2</requirement> </requirements> <command><![CDATA[ qiime feature-table filter-samples --i-table=$itable #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($input_files_mmetadatafile) #end if #if str($pminfrequency): --p-min-frequency=$pminfrequency #end if #if str($pmaxfrequency): --p-max-frequency="$pmaxfrequency" #end if #if str($pminfeatures): --p-min-features=$pminfeatures #end if #if str($pmaxfeatures): --p-max-features="$pmaxfeatures" #end if #if '__sq__' in str($pwhere): #set $pwhere_temp = $pwhere.replace('__sq__', "'") #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 ; cp ofilteredtable.qza $ofilteredtable ]]></command> <inputs> <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency¹ | RelativeFrequency² | PresenceAbsence³ | Composition⁴] The feature table from which samples should be filtered. [required]" name="itable" optional="False" type="data"/> <param label="--p-min-frequency: INTEGER The minimum total frequency that a sample 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 sample 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="True" type="integer"/> <param label="--p-min-features: INTEGER The minimum number of features that a sample must have to be retained. [default: 0]" name="pminfeatures" optional="True" type="integer" value="0"/> <param label="--p-max-features: INTEGER The maximum number of features that a sample can have to be retained. If no value is provided this will default to infinity (i.e., no maximum feature filter will be applied). [optional]" name="pmaxfeatures" optional="True" type="integer"/> <param label="--p-where: TEXT SQLite WHERE clause specifying sample metadata criteria that must be met to be included in the filtered feature table. If not provided, all samples in `metadata` that are also in the feature table will be retained. [optional]" name="pwhere" optional="True" type="text"/> <param label="--p-exclude-ids: --p-no-exclude-ids If true, the samples 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"/> <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file"> <param label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [optional]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" /> </repeat> </inputs> <outputs> <data format="qza" label="${tool.name} on ${on_string}: filteredtable.qza" name="ofilteredtable"/> </outputs> <help><![CDATA[ Filter samples from table ######################### Filter samples from table based on frequency and/or metadata. Any features with a frequency of zero after sample filtering will also be removed. See the filtering tutorial on https://docs.qiime2.org for additional details. Parameters ---------- table : FeatureTable[Frequency¹ | RelativeFrequency² | PresenceAbsence³ | Composition⁴] The feature table from which samples should be filtered. min_frequency : Int, optional The minimum total frequency that a sample must have to be retained. max_frequency : Int, optional The maximum total frequency that a sample 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_features : Int, optional The minimum number of features that a sample must have to be retained. max_features : Int, optional The maximum number of features that a sample can have to be retained. If no value is provided this will default to infinity (i.e., no maximum feature filter will be applied). metadata : Metadata, optional 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 feature table. If not provided, all samples in `metadata` that are also in the feature table will be retained. exclude_ids : Bool, optional If true, the samples selected by `metadata` or `where` parameters will be excluded from the filtered table instead of being retained. Returns ------- filtered_table : FeatureTable[Frequency¹ | RelativeFrequency² | PresenceAbsence³ | Composition⁴] The resulting feature table filtered by sample. ]]></help> <macros> <import>qiime_citation.xml</import> </macros> <expand macro="qiime_citation"/> </tool>