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comparison qiime2/qiime_cutadapt_demux-paired.xml @ 0:51b9b6b57732 draft

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author florianbegusch
date Thu, 24 May 2018 05:21:07 -0400
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1 <?xml version="1.0" ?>
2 <tool id="qiime_cutadapt_demux-paired" name="qiime cutadapt demux-paired" version="2018.4">
3 <description> - Demultiplex paired-end sequence data with barcodes in- sequence.</description>
4 <requirements>
5 <requirement type="package" version="2018.4">qiime2</requirement>
6 </requirements>
7 <command><![CDATA[
8
9 qiime cutadapt demux-paired --i-seqs=$iseqs
10
11 #def list_dict_to_string(list_dict):
12 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
13 #for d in list_dict[1:]:
14 #set $file_list = $file_list + ',' + d['additional_input'].__getattr__('file_name')
15 #end for
16 #return $file_list
17 #end def
18
19 --m-forward-barcodes-file=$list_dict_to_string($input_files_mforwardbarcodesfile) --m-forward-barcodes-column="$mforwardbarcodescolumn"
20
21 #if str($cmdconfig) != 'None':
22 --cmd-config=$cmdconfig
23 #end if
24
25 --o-per-sample-sequences=opersamplesequences --o-untrimmed-sequences=ountrimmedsequences
26
27 #if $perrorrate:
28 --p-error-rate=$perrorrate
29 #end if
30 ;
31
32 cp opersamplesequences.qza $opersamplesequences;
33 cp ountrimmedsequences.qza $ountrimmedsequences;
34
35 ]]></command>
36 <inputs>
37 <param format="qza,no_unzip.zip" label="--i-seqs: Multiplexed Paired End Barcode In Sequence - The paired-end sequences to be demultiplexed. [required]" name="iseqs" optional="False" type="data"/>
38 <repeat name="input_files_mforwardbarcodesfile" optional="False" title="--m-forward-barcodes-file">
39 <param label="--m-forward-barcodes-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [required]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
40 </repeat>
41 <param label="--m-forward-barcodes-column: Metadata Column[Categorical] - Column from metadata file or artifact viewable as metadata. The sample metadata column listing the per-sample barcodes for the forward reads. [required]" name="mforwardbarcodescolumn" optional="False" type="text"/>
42 <param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
43 <param label="--p-error-rate: The level of error tolerance, specified as the maximum allowable error rate. [default: 0.1]" name="perrorrate" optional="True" type="float" value="0.1"/>
44 </inputs>
45 <outputs>
46 <data format="qza" label="${tool.name} on ${on_string}: per-sample-sequences.qza" name="opersamplesequences"/>
47 <data format="qza" label="${tool.name} on ${on_string}: untrimmed-sequences.qza" name="ountrimmedsequences"/>
48 </outputs>
49 <help><![CDATA[
50
51 Demultiplex paired-end sequence data with barcodes in-sequence.
52 ---------------------------------------------------------------
53
54 Demultiplex sequence data (i.e., map barcode reads to sample ids). Barcodes
55 are expected to be located within the sequence data (versus the header, or
56 a separate barcode file).
57
58 Parameters
59 ----------
60 seqs : MultiplexedPairedEndBarcodeInSequence
61 The paired-end sequences to be demultiplexed.
62 forward_barcodes : MetadataColumn[Categorical]
63 The sample metadata column listing the per-sample barcodes for the
64 forward reads.
65 error_rate : Float % Range(0, 1, inclusive_end=True), optional
66 The level of error tolerance, specified as the maximum allowable error
67 rate.
68
69 Returns
70 -------
71 per_sample_sequences : SampleData[PairedEndSequencesWithQuality]
72 The resulting demultiplexed sequences.
73 untrimmed_sequences : MultiplexedPairedEndBarcodeInSequence
74 The sequences that were unmatched to barcodes.
75
76 ]]>
77 </help>
78 <macros>
79 <import>qiime_citation.xml</import>
80 </macros>
81 <expand macro="qiime_citation" />
82 </tool>