annotate qiime2-2020.8/qiime_cutadapt_demux-single.xml @ 0:5c352d975ef7 draft

Uploaded
author florianbegusch
date Thu, 03 Sep 2020 09:33:04 +0000
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
5c352d975ef7 Uploaded
florianbegusch
parents:
diff changeset
1 <?xml version="1.0" ?>
5c352d975ef7 Uploaded
florianbegusch
parents:
diff changeset
2 <tool id="qiime_cutadapt_demux-single" name="qiime cutadapt demux-single"
5c352d975ef7 Uploaded
florianbegusch
parents:
diff changeset
3 version="2020.8">
5c352d975ef7 Uploaded
florianbegusch
parents:
diff changeset
4 <description>Demultiplex single-end sequence data with barcodes in- sequence.</description>
5c352d975ef7 Uploaded
florianbegusch
parents:
diff changeset
5 <requirements>
5c352d975ef7 Uploaded
florianbegusch
parents:
diff changeset
6 <requirement type="package" version="2020.8">qiime2</requirement>
5c352d975ef7 Uploaded
florianbegusch
parents:
diff changeset
7 </requirements>
5c352d975ef7 Uploaded
florianbegusch
parents:
diff changeset
8 <command><![CDATA[
5c352d975ef7 Uploaded
florianbegusch
parents:
diff changeset
9 qiime cutadapt demux-single
5c352d975ef7 Uploaded
florianbegusch
parents:
diff changeset
10
5c352d975ef7 Uploaded
florianbegusch
parents:
diff changeset
11 --i-seqs=$iseqs
5c352d975ef7 Uploaded
florianbegusch
parents:
diff changeset
12 # if $input_files_mbarcodesfile:
5c352d975ef7 Uploaded
florianbegusch
parents:
diff changeset
13 # def list_dict_to_string(list_dict):
5c352d975ef7 Uploaded
florianbegusch
parents:
diff changeset
14 # set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
5c352d975ef7 Uploaded
florianbegusch
parents:
diff changeset
15 # for d in list_dict[1:]:
5c352d975ef7 Uploaded
florianbegusch
parents:
diff changeset
16 # set $file_list = $file_list + ' --m-barcodes-file=' + d['additional_input'].__getattr__('file_name')
5c352d975ef7 Uploaded
florianbegusch
parents:
diff changeset
17 # end for
5c352d975ef7 Uploaded
florianbegusch
parents:
diff changeset
18 # return $file_list
5c352d975ef7 Uploaded
florianbegusch
parents:
diff changeset
19 # end def
5c352d975ef7 Uploaded
florianbegusch
parents:
diff changeset
20 --m-barcodes-file=$list_dict_to_string($input_files_mbarcodesfile)
5c352d975ef7 Uploaded
florianbegusch
parents:
diff changeset
21 # end if
5c352d975ef7 Uploaded
florianbegusch
parents:
diff changeset
22
5c352d975ef7 Uploaded
florianbegusch
parents:
diff changeset
23 #if '__ob__' in str($mbarcodescolumn):
5c352d975ef7 Uploaded
florianbegusch
parents:
diff changeset
24 #set $mbarcodescolumn_temp = $mbarcodescolumn.replace('__ob__', '[')
5c352d975ef7 Uploaded
florianbegusch
parents:
diff changeset
25 #set $mbarcodescolumn = $mbarcodescolumn_temp
5c352d975ef7 Uploaded
florianbegusch
parents:
diff changeset
26 #end if
5c352d975ef7 Uploaded
florianbegusch
parents:
diff changeset
27 #if '__cb__' in str($mbarcodescolumn):
5c352d975ef7 Uploaded
florianbegusch
parents:
diff changeset
28 #set $mbarcodescolumn_temp = $mbarcodescolumn.replace('__cb__', ']')
5c352d975ef7 Uploaded
florianbegusch
parents:
diff changeset
29 #set $mbarcodescolumn = $mbarcodescolumn_temp
5c352d975ef7 Uploaded
florianbegusch
parents:
diff changeset
30 #end if
5c352d975ef7 Uploaded
florianbegusch
parents:
diff changeset
31 #if 'X' in str($mbarcodescolumn):
5c352d975ef7 Uploaded
florianbegusch
parents:
diff changeset
32 #set $mbarcodescolumn_temp = $mbarcodescolumn.replace('X', '\\')
5c352d975ef7 Uploaded
florianbegusch
parents:
diff changeset
33 #set $mbarcodescolumn = $mbarcodescolumn_temp
5c352d975ef7 Uploaded
florianbegusch
parents:
diff changeset
34 #end if
5c352d975ef7 Uploaded
florianbegusch
parents:
diff changeset
35 #if '__sq__' in str($mbarcodescolumn):
5c352d975ef7 Uploaded
florianbegusch
parents:
diff changeset
36 #set $mbarcodescolumn_temp = $mbarcodescolumn.replace('__sq__', "'")
5c352d975ef7 Uploaded
florianbegusch
parents:
diff changeset
37 #set $mbarcodescolumn = $mbarcodescolumn_temp
5c352d975ef7 Uploaded
florianbegusch
parents:
diff changeset
38 #end if
5c352d975ef7 Uploaded
florianbegusch
parents:
diff changeset
39 #if '__db__' in str($mbarcodescolumn):
5c352d975ef7 Uploaded
florianbegusch
parents:
diff changeset
40 #set $mbarcodescolumn_temp = $mbarcodescolumn.replace('__db__', '"')
5c352d975ef7 Uploaded
florianbegusch
parents:
diff changeset
41 #set $mbarcodescolumn = $mbarcodescolumn_temp
5c352d975ef7 Uploaded
florianbegusch
parents:
diff changeset
42 #end if
5c352d975ef7 Uploaded
florianbegusch
parents:
diff changeset
43
5c352d975ef7 Uploaded
florianbegusch
parents:
diff changeset
44 --m-barcodes-column=$mbarcodescolumn
5c352d975ef7 Uploaded
florianbegusch
parents:
diff changeset
45
5c352d975ef7 Uploaded
florianbegusch
parents:
diff changeset
46
5c352d975ef7 Uploaded
florianbegusch
parents:
diff changeset
47 --p-error-rate=$perrorrate
5c352d975ef7 Uploaded
florianbegusch
parents:
diff changeset
48
5c352d975ef7 Uploaded
florianbegusch
parents:
diff changeset
49 --p-minimum-length=$pminimumlength
5c352d975ef7 Uploaded
florianbegusch
parents:
diff changeset
50
5c352d975ef7 Uploaded
florianbegusch
parents:
diff changeset
51 --o-per-sample-sequences=opersamplesequences
5c352d975ef7 Uploaded
florianbegusch
parents:
diff changeset
52
5c352d975ef7 Uploaded
florianbegusch
parents:
diff changeset
53 --o-untrimmed-sequences=ountrimmedsequences
5c352d975ef7 Uploaded
florianbegusch
parents:
diff changeset
54
5c352d975ef7 Uploaded
florianbegusch
parents:
diff changeset
55 #if str($examples) != 'None':
5c352d975ef7 Uploaded
florianbegusch
parents:
diff changeset
56 --examples=$examples
5c352d975ef7 Uploaded
florianbegusch
parents:
diff changeset
57 #end if
5c352d975ef7 Uploaded
florianbegusch
parents:
diff changeset
58
5c352d975ef7 Uploaded
florianbegusch
parents:
diff changeset
59 ;
5c352d975ef7 Uploaded
florianbegusch
parents:
diff changeset
60 cp ountrimmedsequences.qza $ountrimmedsequences
5c352d975ef7 Uploaded
florianbegusch
parents:
diff changeset
61
5c352d975ef7 Uploaded
florianbegusch
parents:
diff changeset
62 ]]></command>
5c352d975ef7 Uploaded
florianbegusch
parents:
diff changeset
63 <inputs>
5c352d975ef7 Uploaded
florianbegusch
parents:
diff changeset
64 <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" />
5c352d975ef7 Uploaded
florianbegusch
parents:
diff changeset
65 <repeat name="input_files_mbarcodesfile" optional="True" title="--m-barcodes-file">
5c352d975ef7 Uploaded
florianbegusch
parents:
diff changeset
66 <param format="tabular,qza,no_unzip.zip" label="--m-barcodes-file: METADATA" name="additional_input" optional="True" type="data" />
5c352d975ef7 Uploaded
florianbegusch
parents:
diff changeset
67 </repeat>
5c352d975ef7 Uploaded
florianbegusch
parents:
diff changeset
68 <param label="--m-barcodes-column: COLUMN MetadataColumn[Categorical] The sample metadata column listing the per-sample barcodes. [required]" name="mbarcodescolumn" optional="False" type="text" />
5c352d975ef7 Uploaded
florianbegusch
parents:
diff changeset
69 <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" />
5c352d975ef7 Uploaded
florianbegusch
parents:
diff changeset
70 <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" />
5c352d975ef7 Uploaded
florianbegusch
parents:
diff changeset
71 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
5c352d975ef7 Uploaded
florianbegusch
parents:
diff changeset
72
5c352d975ef7 Uploaded
florianbegusch
parents:
diff changeset
73 </inputs>
5c352d975ef7 Uploaded
florianbegusch
parents:
diff changeset
74
5c352d975ef7 Uploaded
florianbegusch
parents:
diff changeset
75 <outputs>
5c352d975ef7 Uploaded
florianbegusch
parents:
diff changeset
76 <data format="qza" label="${tool.name} on ${on_string}: persamplesequences.qza" name="opersamplesequences" />
5c352d975ef7 Uploaded
florianbegusch
parents:
diff changeset
77 <data format="qza" label="${tool.name} on ${on_string}: untrimmedsequences.qza" name="ountrimmedsequences" />
5c352d975ef7 Uploaded
florianbegusch
parents:
diff changeset
78
5c352d975ef7 Uploaded
florianbegusch
parents:
diff changeset
79 </outputs>
5c352d975ef7 Uploaded
florianbegusch
parents:
diff changeset
80
5c352d975ef7 Uploaded
florianbegusch
parents:
diff changeset
81 <help><![CDATA[
5c352d975ef7 Uploaded
florianbegusch
parents:
diff changeset
82 Demultiplex single-end sequence data with barcodes in- sequence.
5c352d975ef7 Uploaded
florianbegusch
parents:
diff changeset
83 ###############################################################
5c352d975ef7 Uploaded
florianbegusch
parents:
diff changeset
84
5c352d975ef7 Uploaded
florianbegusch
parents:
diff changeset
85 Demultiplex sequence data (i.e., map barcode reads to sample ids). Barcodes
5c352d975ef7 Uploaded
florianbegusch
parents:
diff changeset
86 are expected to be located within the sequence data (versus the header, or
5c352d975ef7 Uploaded
florianbegusch
parents:
diff changeset
87 a separate barcode file).
5c352d975ef7 Uploaded
florianbegusch
parents:
diff changeset
88
5c352d975ef7 Uploaded
florianbegusch
parents:
diff changeset
89 Parameters
5c352d975ef7 Uploaded
florianbegusch
parents:
diff changeset
90 ----------
5c352d975ef7 Uploaded
florianbegusch
parents:
diff changeset
91 seqs : MultiplexedSingleEndBarcodeInSequence
5c352d975ef7 Uploaded
florianbegusch
parents:
diff changeset
92 The single-end sequences to be demultiplexed.
5c352d975ef7 Uploaded
florianbegusch
parents:
diff changeset
93 barcodes : MetadataColumn[Categorical]
5c352d975ef7 Uploaded
florianbegusch
parents:
diff changeset
94 The sample metadata column listing the per-sample barcodes.
5c352d975ef7 Uploaded
florianbegusch
parents:
diff changeset
95 error_rate : Float % Range(0, 1, inclusive_end=True), optional
5c352d975ef7 Uploaded
florianbegusch
parents:
diff changeset
96 The level of error tolerance, specified as the maximum allowable error
5c352d975ef7 Uploaded
florianbegusch
parents:
diff changeset
97 rate. The default value specified by cutadapt is 0.1 (=10%), which is
5c352d975ef7 Uploaded
florianbegusch
parents:
diff changeset
98 greater than `demux emp-*`, which is 0.0 (=0%).
5c352d975ef7 Uploaded
florianbegusch
parents:
diff changeset
99 batch_size : Int % Range(0, None), optional
5c352d975ef7 Uploaded
florianbegusch
parents:
diff changeset
100 The number of samples cutadapt demultiplexes concurrently.
5c352d975ef7 Uploaded
florianbegusch
parents:
diff changeset
101 Demultiplexing in smaller batches will yield the same result with
5c352d975ef7 Uploaded
florianbegusch
parents:
diff changeset
102 marginal speed loss, and may solve "too many files" errors related to
5c352d975ef7 Uploaded
florianbegusch
parents:
diff changeset
103 sample quantity. Set to "0" to process all samples at once.
5c352d975ef7 Uploaded
florianbegusch
parents:
diff changeset
104 minimum_length : Int % Range(1, None), optional
5c352d975ef7 Uploaded
florianbegusch
parents:
diff changeset
105 Discard reads shorter than specified value. Note, the cutadapt default
5c352d975ef7 Uploaded
florianbegusch
parents:
diff changeset
106 of 0 has been overridden, because that value produces empty sequence
5c352d975ef7 Uploaded
florianbegusch
parents:
diff changeset
107 records.
5c352d975ef7 Uploaded
florianbegusch
parents:
diff changeset
108
5c352d975ef7 Uploaded
florianbegusch
parents:
diff changeset
109 Returns
5c352d975ef7 Uploaded
florianbegusch
parents:
diff changeset
110 -------
5c352d975ef7 Uploaded
florianbegusch
parents:
diff changeset
111 per_sample_sequences : SampleData[SequencesWithQuality]
5c352d975ef7 Uploaded
florianbegusch
parents:
diff changeset
112 The resulting demultiplexed sequences.
5c352d975ef7 Uploaded
florianbegusch
parents:
diff changeset
113 untrimmed_sequences : MultiplexedSingleEndBarcodeInSequence
5c352d975ef7 Uploaded
florianbegusch
parents:
diff changeset
114 The sequences that were unmatched to barcodes.
5c352d975ef7 Uploaded
florianbegusch
parents:
diff changeset
115 ]]></help>
5c352d975ef7 Uploaded
florianbegusch
parents:
diff changeset
116 <macros>
5c352d975ef7 Uploaded
florianbegusch
parents:
diff changeset
117 <import>qiime_citation.xml</import>
5c352d975ef7 Uploaded
florianbegusch
parents:
diff changeset
118 </macros>
5c352d975ef7 Uploaded
florianbegusch
parents:
diff changeset
119 <expand macro="qiime_citation"/>
5c352d975ef7 Uploaded
florianbegusch
parents:
diff changeset
120 </tool>