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view qiime2/qiime_diversity_filter-distance-matrix.xml @ 1:255f48db74f8 draft
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author | florianbegusch |
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date | Wed, 17 Jul 2019 03:26:16 -0400 |
parents | 370e0b6e9826 |
children | 914fa4daf16a |
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<?xml version="1.0" ?> <tool id="qiime_diversity_filter-distance-matrix" name="qiime diversity filter-distance-matrix" version="2019.4"> <description> - Filter samples from a distance matrix.</description> <requirements> <requirement type="package" version="2019.4">qiime2</requirement> </requirements> <command><![CDATA[ qiime diversity filter-distance-matrix --i-distance-matrix=$idistancematrix #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($input_files_mmetadatafile) #end if #if '__sq__' in str($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-distance-matrix=ofiltereddistancematrix ; cp ofiltereddistancematrix.qza $ofiltereddistancematrix ]]></command> <inputs> <param format="qza,no_unzip.zip" label="--i-distance-matrix: ARTIFACT DistanceMatrix Distance matrix to filter by sample. [required]" name="idistancematrix" optional="False" type="data"/> <param label="--p-where: TEXT SQLite WHERE clause specifying sample metadata criteria that must be met to be included in the filtered distance matrix. If not provided, all samples in `metadata` that are also in the input distance matrix will be retained. [optional]" name="pwhere" optional="True" type="text"/> <param label="--p-exclude-ids: --p-no-exclude-ids If `True`, the samples selected by `metadata` or `where` parameters will be excluded from the filtered distance matrix instead of being retained. [default: False]" name="pexcludeids" selected="False" type="boolean"/> <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file"> <param label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [optional]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" /> </repeat> </inputs> <outputs> <data format="qza" label="${tool.name} on ${on_string}: filtereddistancematrix.qza" name="ofiltereddistancematrix"/> </outputs> <help><![CDATA[ Filter samples from a distance matrix. ###################################### Filter samples from a distance matrix, retaining only the samples matching search criteria specified by `metadata` and `where` parameters (or retaining only the samples not matching that criteria, if `exclude_ids` is True). See the filtering tutorial on https://docs.qiime2.org for additional details. Parameters ---------- distance_matrix : DistanceMatrix Distance matrix to filter by sample. metadata : Metadata 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 distance matrix. If not provided, all samples in `metadata` that are also in the input distance matrix will be retained. exclude_ids : Bool, optional If `True`, the samples selected by `metadata` or `where` parameters will be excluded from the filtered distance matrix instead of being retained. Returns ------- filtered_distance_matrix : DistanceMatrix Distance matrix filtered to include samples matching search criteria ]]></help> <macros> <import>qiime_citation.xml</import> </macros> <expand macro="qiime_citation"/> </tool>