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view qiime2-2020.8/qiime_demux_emp-paired.xml @ 22:292c84bd5ab6 draft
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author | florianbegusch |
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date | Fri, 04 Sep 2020 12:55:05 +0000 |
parents | d93d8888f0b0 |
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<?xml version="1.0" ?> <tool id="qiime_demux_emp-paired" name="qiime demux emp-paired" version="2020.8"> <description>Demultiplex paired-end sequence data generated with the EMP protocol.</description> <requirements> <requirement type="package" version="2020.8">qiime2</requirement> </requirements> <command><![CDATA[ qiime demux emp-paired --i-seqs=$iseqs # if $input_files_mbarcodesfile: # 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-barcodes-file=' + d['additional_input'].__getattr__('file_name') # end for # return $file_list # end def --m-barcodes-file=$list_dict_to_string($input_files_mbarcodesfile) # end if #if '__ob__' in str($mbarcodescolumn): #set $mbarcodescolumn_temp = $mbarcodescolumn.replace('__ob__', '[') #set $mbarcodescolumn = $mbarcodescolumn_temp #end if #if '__cb__' in str($mbarcodescolumn): #set $mbarcodescolumn_temp = $mbarcodescolumn.replace('__cb__', ']') #set $mbarcodescolumn = $mbarcodescolumn_temp #end if #if 'X' in str($mbarcodescolumn): #set $mbarcodescolumn_temp = $mbarcodescolumn.replace('X', '\\') #set $mbarcodescolumn = $mbarcodescolumn_temp #end if #if '__sq__' in str($mbarcodescolumn): #set $mbarcodescolumn_temp = $mbarcodescolumn.replace('__sq__', "'") #set $mbarcodescolumn = $mbarcodescolumn_temp #end if #if '__db__' in str($mbarcodescolumn): #set $mbarcodescolumn_temp = $mbarcodescolumn.replace('__db__', '"') #set $mbarcodescolumn = $mbarcodescolumn_temp #end if --m-barcodes-column=$mbarcodescolumn #if $pnogolayerrorcorrection: --p-no-golay-error-correction #end if #if $prevcompbarcodes: --p-rev-comp-barcodes #end if #if $prevcompmappingbarcodes: --p-rev-comp-mapping-barcodes #end if --o-per-sample-sequences=opersamplesequences --o-error-correction-details=oerrorcorrectiondetails #if str($examples) != 'None': --examples=$examples #end if ; cp oerrorcorrectiondetails.qza $oerrorcorrectiondetails ]]></command> <inputs> <param format="qza,no_unzip.zip" label="--i-seqs: ARTIFACT EMPPairedEndSequences The paired-end sequences to be demultiplexed. [required]" name="iseqs" optional="False" type="data" /> <repeat name="input_files_mbarcodesfile" optional="True" title="--m-barcodes-file"> <param format="tabular,qza,no_unzip.zip" label="--m-barcodes-file: METADATA" name="additional_input" optional="True" type="data" /> </repeat> <param label="--m-barcodes-column: COLUMN MetadataColumn[Categorical] The sample metadata column containing the per-sample barcodes. [required]" name="mbarcodescolumn" optional="False" type="text" /> <param label="--p-no-golay-error-correction: Do not perform 12nt Golay error correction on the barcode reads. [default: True]" name="pnogolayerrorcorrection" selected="False" type="boolean" /> <param format="tabular,qza,no_unzip.zip" label="--p-rev-comp-barcodes: --p-rev-comp-barcodes: / --p-no-rev-comp-barcodes If provided, the barcode sequence reads will be reverse complemented prior to demultiplexing. [default: False]" name="prevcompbarcodes" selected="False" type="boolean" /> <param format="tabular,qza,no_unzip.zip" label="--p-rev-comp-mapping-barcodes: --p-rev-comp-mapping-barcodes: / --p-no-rev-comp-mapping-barcodes If provided, the barcode sequences in the sample metadata will be reverse complemented prior to demultiplexing. [default: False]" name="prevcompmappingbarcodes" selected="False" type="boolean" /> <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" /> </inputs> <outputs> <data format="qza" label="${tool.name} on ${on_string}: persamplesequences.qza" name="opersamplesequences" /> <data format="qza" label="${tool.name} on ${on_string}: errorcorrectiondetails.qza" name="oerrorcorrectiondetails" /> </outputs> <help><![CDATA[ Demultiplex paired-end sequence data generated with the EMP protocol. ############################################################### Demultiplex paired-end sequence data (i.e., map barcode reads to sample ids) for data generated with the Earth Microbiome Project (EMP) amplicon sequencing protocol. Details about this protocol can be found at http://www.earthmicrobiome.org/protocols-and-standards/ Parameters ---------- seqs : EMPPairedEndSequences The paired-end sequences to be demultiplexed. barcodes : MetadataColumn[Categorical] The sample metadata column containing the per-sample barcodes. golay_error_correction : Bool, optional Perform 12nt Golay error correction on the barcode reads. rev_comp_barcodes : Bool, optional If provided, the barcode sequence reads will be reverse complemented prior to demultiplexing. rev_comp_mapping_barcodes : Bool, optional If provided, the barcode sequences in the sample metadata will be reverse complemented prior to demultiplexing. Returns ------- per_sample_sequences : SampleData[PairedEndSequencesWithQuality] The resulting demultiplexed sequences. error_correction_details : ErrorCorrectionDetails Detail about the barcode error corrections. ]]></help> <macros> <import>qiime_citation.xml</import> </macros> <expand macro="qiime_citation"/> </tool>