Mercurial > repos > florianbegusch > qiime2_suite

comparison qiime2/qiime_cutadapt_demux-paired.xml @ 29:3ba9833030c1 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author florianbegusch
date Fri, 04 Sep 2020 13:12:49 +0000
parents
children
comparison
equal deleted inserted replaced
28:c28331a63dfd 29:3ba9833030c1
1 <?xml version="1.0" ?>
2 <tool id="qiime_cutadapt_demux-paired" name="qiime cutadapt demux-paired"
3 version="2020.8">
4 <description>Demultiplex paired-end sequence data with barcodes in- sequence.</description>
5 <requirements>
6 <requirement type="package" version="2020.8">qiime2</requirement>
7 </requirements>
8 <command><![CDATA[
9 qiime cutadapt demux-paired
10
11 --i-seqs=$iseqs
12 # if $input_files_mforwardbarcodesfile:
13 # def list_dict_to_string(list_dict):
14 # set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
15 # for d in list_dict[1:]:
16 # set $file_list = $file_list + ' --m-forward-barcodes-file=' + d['additional_input'].__getattr__('file_name')
17 # end for
18 # return $file_list
19 # end def
20 --m-forward-barcodes-file=$list_dict_to_string($input_files_mforwardbarcodesfile)
21 # end if
22
23 #if '__ob__' in str($mforwardbarcodescolumn):
24 #set $mforwardbarcodescolumn_temp = $mforwardbarcodescolumn.replace('__ob__', '[')
25 #set $mforwardbarcodescolumn = $mforwardbarcodescolumn_temp
26 #end if
27 #if '__cb__' in str($mforwardbarcodescolumn):
28 #set $mforwardbarcodescolumn_temp = $mforwardbarcodescolumn.replace('__cb__', ']')
29 #set $mforwardbarcodescolumn = $mforwardbarcodescolumn_temp
30 #end if
31 #if 'X' in str($mforwardbarcodescolumn):
32 #set $mforwardbarcodescolumn_temp = $mforwardbarcodescolumn.replace('X', '\\')
33 #set $mforwardbarcodescolumn = $mforwardbarcodescolumn_temp
34 #end if
35 #if '__sq__' in str($mforwardbarcodescolumn):
36 #set $mforwardbarcodescolumn_temp = $mforwardbarcodescolumn.replace('__sq__', "'")
37 #set $mforwardbarcodescolumn = $mforwardbarcodescolumn_temp
38 #end if
39 #if '__db__' in str($mforwardbarcodescolumn):
40 #set $mforwardbarcodescolumn_temp = $mforwardbarcodescolumn.replace('__db__', '"')
41 #set $mforwardbarcodescolumn = $mforwardbarcodescolumn_temp
42 #end if
43
44 --m-forward-barcodes-column=$mforwardbarcodescolumn
45
46 # if $input_files_mreversebarcodesfile:
47 # def list_dict_to_string(list_dict):
48 # set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
49 # for d in list_dict[1:]:
50 # set $file_list = $file_list + ' --m-reverse-barcodes-file=' + d['additional_input'].__getattr__('file_name')
51 # end for
52 # return $file_list
53 # end def
54 --m-reverse-barcodes-file=$list_dict_to_string($input_files_mreversebarcodesfile)
55 # end if
56
57 #if '__ob__' in str($mreversebarcodescolumn):
58 #set $mreversebarcodescolumn_temp = $mreversebarcodescolumn.replace('__ob__', '[')
59 #set $mreversebarcodescolumn = $mreversebarcodescolumn_temp
60 #end if
61 #if '__cb__' in str($mreversebarcodescolumn):
62 #set $mreversebarcodescolumn_temp = $mreversebarcodescolumn.replace('__cb__', ']')
63 #set $mreversebarcodescolumn = $mreversebarcodescolumn_temp
64 #end if
65 #if 'X' in str($mreversebarcodescolumn):
66 #set $mreversebarcodescolumn_temp = $mreversebarcodescolumn.replace('X', '\\')
67 #set $mreversebarcodescolumn = $mreversebarcodescolumn_temp
68 #end if
69 #if '__sq__' in str($mreversebarcodescolumn):
70 #set $mreversebarcodescolumn_temp = $mreversebarcodescolumn.replace('__sq__', "'")
71 #set $mreversebarcodescolumn = $mreversebarcodescolumn_temp
72 #end if
73 #if '__db__' in str($mreversebarcodescolumn):
74 #set $mreversebarcodescolumn_temp = $mreversebarcodescolumn.replace('__db__', '"')
75 #set $mreversebarcodescolumn = $mreversebarcodescolumn_temp
76 #end if
77
78 #if str($mreversebarcodescolumn):
79 --m-reverse-barcodes-column=$mreversebarcodescolumn
80 #end if
81
82 --p-error-rate=$perrorrate
83
84 --p-minimum-length=$pminimumlength
85
86 #if $pmixedorientation:
87 --p-mixed-orientation
88 #end if
89
90 --o-per-sample-sequences=opersamplesequences
91
92 --o-untrimmed-sequences=ountrimmedsequences
93
94 #if str($examples) != 'None':
95 --examples=$examples
96 #end if
97
98 ;
99 cp ountrimmedsequences.qza $ountrimmedsequences
100
101 ]]></command>
102 <inputs>
103 <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" />
104 <repeat name="input_files_mforwardbarcodesfile" optional="True" title="--m-forward-barcodes-file">
105 <param format="tabular,qza,no_unzip.zip" label="--m-forward-barcodes-file: METADATA" name="additional_input" optional="True" type="data" />
106 </repeat>
107 <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" />
108 <repeat name="input_files_mreversebarcodesfile" optional="True" title="--m-reverse-barcodes-file">
109 <param format="tabular,qza,no_unzip.zip" label="--m-reverse-barcodes-file: METADATA" name="additional_input" optional="True" type="data" />
110 </repeat>
111 <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="False" type="text" />
112 <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. [default: 0.1]" max="1" min="0" name="perrorrate" optional="True" type="float" value="0.1" />
113 <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" />
114 <param label="--p-mixed-orientation: --p-mixed-orientation: / --p-no-mixed-orientation Handle demultiplexing of mixed orientation reads (i.e. when forward and reverse reads coexist in the same file). [default: False]" name="pmixedorientation" selected="False" type="boolean" />
115 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
116
117 </inputs>
118
119 <outputs>
120 <data format="qza" label="${tool.name} on ${on_string}: persamplesequences.qza" name="opersamplesequences" />
121 <data format="qza" label="${tool.name} on ${on_string}: untrimmedsequences.qza" name="ountrimmedsequences" />
122
123 </outputs>
124
125 <help><![CDATA[
126 Demultiplex paired-end sequence data with barcodes in- sequence.
127 ###############################################################
128
129 Demultiplex sequence data (i.e., map barcode reads to sample ids). Barcodes
130 are expected to be located within the sequence data (versus the header, or
131 a separate barcode file).
132
133 Parameters
134 ----------
135 seqs : MultiplexedPairedEndBarcodeInSequence
136 The paired-end sequences to be demultiplexed.
137 forward_barcodes : MetadataColumn[Categorical]
138 The sample metadata column listing the per-sample barcodes for the
139 forward reads.
140 reverse_barcodes : MetadataColumn[Categorical], optional
141 The sample metadata column listing the per-sample barcodes for the
142 reverse reads.
143 error_rate : Float % Range(0, 1, inclusive_end=True), optional
144 The level of error tolerance, specified as the maximum allowable error
145 rate.
146 batch_size : Int % Range(0, None), optional
147 The number of samples cutadapt demultiplexes concurrently.
148 Demultiplexing in smaller batches will yield the same result with
149 marginal speed loss, and may solve "too many files" errors related to
150 sample quantity. Set to "0" to process all samples at once.
151 minimum_length : Int % Range(1, None), optional
152 Discard reads shorter than specified value. Note, the cutadapt default
153 of 0 has been overridden, because that value produces empty sequence
154 records.
155 mixed_orientation : Bool, optional
156 Handle demultiplexing of mixed orientation reads (i.e. when forward and
157 reverse reads coexist in the same file).
158
159 Returns
160 -------
161 per_sample_sequences : SampleData[PairedEndSequencesWithQuality]
162 The resulting demultiplexed sequences.
163 untrimmed_sequences : MultiplexedPairedEndBarcodeInSequence
164 The sequences that were unmatched to barcodes.
165 ]]></help>
166 <macros>
167 <import>qiime_citation.xml</import>
168 </macros>
169 <expand macro="qiime_citation"/>
170 </tool>