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comparison qiime2/qiime_cutadapt_demux-paired.xml @ 0:370e0b6e9826 draft

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author florianbegusch
date Wed, 17 Jul 2019 03:05:17 -0400
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1 <?xml version="1.0" ?>
2 <tool id="qiime_cutadapt_demux-paired" name="qiime cutadapt demux-paired" version="2019.4">
3 <description> - Demultiplex paired-end sequence data with barcodes in- sequence.</description>
4 <requirements>
5 <requirement type="package" version="2019.4">qiime2</requirement>
6 </requirements>
7 <command><![CDATA[
8 qiime cutadapt demux-paired
9 --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("$input_files_mforwardbarcodesfile")
20 --m-reverse-barcodes-file=$list_dict_to_string("$input_files_mreversebarcodesfile")
21
22 --m-forward-barcodes-column="$mforwardbarcodescolumn"
23
24 #if str($mreversebarcodescolumn):
25 --m-reverse-barcodes-column="$mreversebarcodescolumn"
26 #end if
27
28 #if $perrorrate:
29 --p-error-rate=$perrorrate
30 #end if
31
32
33 --o-per-sample-sequences=opersamplesequences
34 --o-untrimmed-sequences=ountrimmedsequences
35 ;
36
37 cp opersamplesequences.qza $opersamplesequences;
38 cp ountrimmedsequences.qza $ountrimmedsequences
39 ]]></command>
40 <inputs>
41 <param format="qza,no_unzip.zip" label="--i-seqs: ARTIFACT MultiplexedPairedEndBarcodeInSequence The paired-end sequences to be demultiplexed. [required]" name="iseqs" optional="False" type="data"/>
42 <param label="--m-forward-barcodes-column: COLUMN MetadataColumn[Categorical] The sample metadata column listing the per-sample barcodes for the forward reads. [required]" name="mforwardbarcodescolumn" optional="False" type="text"/>
43 <param label="--m-reverse-barcodes-column: COLUMN MetadataColumn[Categorical] The sample metadata column listing the per-sample barcodes for the reverse reads. [optional]" name="mreversebarcodescolumn" optional="True" type="text"/>
44
45 <repeat name="input_files_mforwardbarcodesfile" optional="False" title="--m-forward-barcodes-file">
46 <param label="--m-forward-barcodes-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [required]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
47 </repeat>
48
49 <repeat name="input_files_mreversebarcodesfile" optional="False" title="--m-reverse-barcodes-file">
50 <param label="--m-reverse-barcodes-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [required]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
51 </repeat>
52
53 <param label="--p-error-rate: PROPORTION Range(0, 1, inclusive_end=True) The level of error tolerance, specified as the maximum allowable error rate. [default: 0.1]" name="perrorrate" optional="True" type="float" min="0" max="1" exclude_max="False" value="0.1"/>
54 </inputs>
55 <outputs>
56 <data format="qza" label="${tool.name} on ${on_string}: persamplesequences.qza" name="opersamplesequences"/>
57 <data format="qza" label="${tool.name} on ${on_string}: untrimmedsequences.qza" name="ountrimmedsequences"/>
58 </outputs>
59 <help><![CDATA[
60 Demultiplex paired-end sequence data with barcodes in-sequence.
61 ###############################################################
62
63 Demultiplex sequence data (i.e., map barcode reads to sample ids). Barcodes
64 are expected to be located within the sequence data (versus the header, or
65 a separate barcode file).
66
67 Parameters
68 ----------
69 seqs : MultiplexedPairedEndBarcodeInSequence
70 The paired-end sequences to be demultiplexed.
71 forward_barcodes : MetadataColumn[Categorical]
72 The sample metadata column listing the per-sample barcodes for the
73 forward reads.
74 reverse_barcodes : MetadataColumn[Categorical], optional
75 The sample metadata column listing the per-sample barcodes for the
76 reverse reads.
77 error_rate : Float % Range(0, 1, inclusive_end=True), optional
78 The level of error tolerance, specified as the maximum allowable error
79 rate.
80
81 Returns
82 -------
83 per_sample_sequences : SampleData[PairedEndSequencesWithQuality]
84 The resulting demultiplexed sequences.
85 untrimmed_sequences : MultiplexedPairedEndBarcodeInSequence
86 The sequences that were unmatched to barcodes.
87 ]]></help>
88 <macros>
89 <import>qiime_citation.xml</import>
90 </macros>
91 <expand macro="qiime_citation"/>
92 </tool>