Mercurial > repos > florianbegusch > qiime2_suite
diff qiime2-2020.8/qiime_cutadapt_demux-single.xml @ 20:d93d8888f0b0 draft
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author | florianbegusch |
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date | Fri, 04 Sep 2020 12:44:24 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2-2020.8/qiime_cutadapt_demux-single.xml Fri Sep 04 12:44:24 2020 +0000 @@ -0,0 +1,120 @@ +<?xml version="1.0" ?> +<tool id="qiime_cutadapt_demux-single" name="qiime cutadapt demux-single" + version="2020.8"> + <description>Demultiplex single-end sequence data with barcodes in- sequence.</description> + <requirements> + <requirement type="package" version="2020.8">qiime2</requirement> + </requirements> + <command><![CDATA[ +qiime cutadapt demux-single + +--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 + + +--p-error-rate=$perrorrate + +--p-minimum-length=$pminimumlength + +--o-per-sample-sequences=opersamplesequences + +--o-untrimmed-sequences=ountrimmedsequences + +#if str($examples) != 'None': +--examples=$examples +#end if + +; +cp ountrimmedsequences.qza $ountrimmedsequences + + ]]></command> + <inputs> + <param format="qza,no_unzip.zip" label="--i-seqs: ARTIFACT MultiplexedSingleEndBarcodeInSequence The single-end sequences to be demultiplexed. [required]" name="iseqs" optional="False" type="data" /> + <repeat name="input_files_mbarcodesfile" optional="True" title="--m-barcodes-file"> + <param format="tabular,qza,no_unzip.zip" label="--m-barcodes-file: METADATA" name="additional_input" optional="True" type="data" /> + </repeat> + <param label="--m-barcodes-column: COLUMN MetadataColumn[Categorical] The sample metadata column listing the per-sample barcodes. [required]" name="mbarcodescolumn" optional="False" type="text" /> + <param exclude_max="False" label="--p-error-rate: PROPORTION Range(0, 1, inclusive_end=True) The level of error tolerance, specified as the maximum allowable error rate. The default value specified by cutadapt is 0.1 (=10%), which is greater than `demux emp-*`, which is 0.0 (=0%). [default: 0.1]" max="1" min="0" name="perrorrate" optional="True" type="float" value="0.1" /> + <param label="--p-minimum-length: INTEGER Range(1, None) Discard reads shorter than specified value. Note, the cutadapt default of 0 has been overridden, because that value produces empty sequence records. [default: 1]" min="1" name="pminimumlength" optional="True" type="integer" value="1" /> + <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" /> + + </inputs> + + <outputs> + <data format="qza" label="${tool.name} on ${on_string}: persamplesequences.qza" name="opersamplesequences" /> + <data format="qza" label="${tool.name} on ${on_string}: untrimmedsequences.qza" name="ountrimmedsequences" /> + + </outputs> + + <help><![CDATA[ +Demultiplex single-end sequence data with barcodes in- sequence. +############################################################### + +Demultiplex sequence data (i.e., map barcode reads to sample ids). Barcodes +are expected to be located within the sequence data (versus the header, or +a separate barcode file). + +Parameters +---------- +seqs : MultiplexedSingleEndBarcodeInSequence + The single-end sequences to be demultiplexed. +barcodes : MetadataColumn[Categorical] + The sample metadata column listing the per-sample barcodes. +error_rate : Float % Range(0, 1, inclusive_end=True), optional + The level of error tolerance, specified as the maximum allowable error + rate. The default value specified by cutadapt is 0.1 (=10%), which is + greater than `demux emp-*`, which is 0.0 (=0%). +batch_size : Int % Range(0, None), optional + The number of samples cutadapt demultiplexes concurrently. + Demultiplexing in smaller batches will yield the same result with + marginal speed loss, and may solve "too many files" errors related to + sample quantity. Set to "0" to process all samples at once. +minimum_length : Int % Range(1, None), optional + Discard reads shorter than specified value. Note, the cutadapt default + of 0 has been overridden, because that value produces empty sequence + records. + +Returns +------- +per_sample_sequences : SampleData[SequencesWithQuality] + The resulting demultiplexed sequences. +untrimmed_sequences : MultiplexedSingleEndBarcodeInSequence + The sequences that were unmatched to barcodes. + ]]></help> + <macros> + <import>qiime_citation.xml</import> + </macros> + <expand macro="qiime_citation"/> +</tool> \ No newline at end of file