Mercurial > repos > florianbegusch > qiime2_suite
view qiime2/qiime_demux_filter-samples.xml @ 6:de4c22a52df4 draft
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author | florianbegusch |
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date | Tue, 13 Aug 2019 07:46:48 -0400 |
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<?xml version="1.0" ?> <tool id="qiime_demux_filter-samples" name="qiime demux filter-samples" version="2019.7"> <description> - Filter samples out of demultiplexed data.</description> <requirements> <requirement type="package" version="2019.7">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($input_files_mmetadatafile) #end if #if '__sq__' in str($pwhere): #set $pwhere_temp = $pwhere.replace('__sq__', "'") #set $pwhere = $pwhere_temp #end if #if str($pwhere): --p-where="$pwhere" #end if #if $pexcludeids: --p-exclude-ids #end if #if str($citations) != 'None': --citations=$citations #end if --o-filtered-demux=ofiltereddemux ; cp ofiltereddemux.qza $ofiltereddemux ]]></command> <inputs> <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file"> <param label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. Sample metadata file containing individual_id_column. [required]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" /> </repeat> <param format="qza,no_unzip.zip" label="--i-demux: ARTIFACT SampleData[SequencesWithQuality¹ | PairedEndSequencesWithQuality² | JoinedSequencesWithQuality³] The demultiplexed data from which samples should be filtered. [required]" name="idemux" optional="False" type="data"/> <param label="--p-where: TEXT Optional SQLite WHERE clause specifying sample metadata criteria that must be met to be included in the filtered data. If not provided, all samples in `metadata` that are also in the demultiplexed data will be retained. [optional]" name="pwhere" optional="True" type="text"/> <param label="--p-exclude-ids: --p-no-exclude-ids Defaults to False. If True, the samples selected by the `metadata` and optional `where` parameter will be excluded from the filtered data. [default: False]" name="pexcludeids" selected="False" type="boolean"/> </inputs> <outputs> <data format="qza" label="${tool.name} on ${on_string}: filtereddemux.qza" name="ofiltereddemux"/> </outputs> <help><![CDATA[ ]]></help> <macros> <import>qiime_citation.xml</import> </macros> <expand macro="qiime_citation"/> </tool>