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comparison qiime2/qiime_dada2_denoise-paired.xml @ 9:f190567fe3f6 draft

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author florianbegusch
date Wed, 14 Aug 2019 15:12:48 -0400
parents de4c22a52df4
children a0a8d77a991c
comparison
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8:d66c7509e8f9 9:f190567fe3f6
1 <?xml version="1.0" ?> 1 <?xml version="1.0" ?>
2 <tool id="qiime_dada2_denoise-paired" name="qiime dada2 denoise-paired" version="2019.4"> 2 <tool id="qiime_dada2_denoise-paired" name="qiime dada2 denoise-paired" version="2019.7">
3 <description> - Denoise and dereplicate paired-end sequences</description> 3 <description> - Denoise and dereplicate paired-end sequences</description>
4 <requirements> 4 <requirements>
5 <requirement type="package" version="2019.4">qiime2</requirement> 5 <requirement type="package" version="2019.7">qiime2</requirement>
6 </requirements> 6 </requirements>
7 <command><![CDATA[ 7 <command><![CDATA[
8 8
9 #def parse_file(file): 9 #def parse_file(file):
10 #import csv 10 #import csv
80 80
81 #if str($ptrimleftr): 81 #if str($ptrimleftr):
82 --p-trim-left-r=$ptrimleftr 82 --p-trim-left-r=$ptrimleftr
83 #end if 83 #end if
84 84
85 #if str($pmaxee): 85
86 --p-max-ee=$pmaxee 86
87 #end if 87
88 #if str($pmaxeef):
89 --p-max-ee-f=$pmaxeef
90 #end if
91
92 #if str($pmaxeer):
93 --p-max-ee-r=$pmaxeer
94 #end if
95
96
97
88 98
89 #if str($ptruncq): 99 #if str($ptruncq):
90 --p-trunc-q=$ptruncq 100 --p-trunc-q=$ptruncq
91 #end if 101 #end if
92 102
128 <param format="qza,no_unzip.zip" label="--i-demultiplexed-seqs: ARTIFACT SampleData[PairedEndSequencesWithQuality] The paired-end demultiplexed sequences to be denoised. [required]" name="idemultiplexedseqs" optional="False" type="data"/> 138 <param format="qza,no_unzip.zip" label="--i-demultiplexed-seqs: ARTIFACT SampleData[PairedEndSequencesWithQuality] The paired-end demultiplexed sequences to be denoised. [required]" name="idemultiplexedseqs" optional="False" type="data"/>
129 <param label="--p-trunc-len-f: INTEGER Position at which forward read sequences should be truncated due to decrease in quality. This truncates the 3' end of the of the input sequences, which will be the bases that were sequenced in the last cycles. Reads that are shorter than this value will be discarded. After this parameter is applied there must still be at least a 20 nucleotide overlap between the forward and reverse reads. If 0 is provided, no truncation or length filtering will be performed [required]" name="ptrunclenf" optional="False" value="" type="integer"/> 139 <param label="--p-trunc-len-f: INTEGER Position at which forward read sequences should be truncated due to decrease in quality. This truncates the 3' end of the of the input sequences, which will be the bases that were sequenced in the last cycles. Reads that are shorter than this value will be discarded. After this parameter is applied there must still be at least a 20 nucleotide overlap between the forward and reverse reads. If 0 is provided, no truncation or length filtering will be performed [required]" name="ptrunclenf" optional="False" value="" type="integer"/>
130 <param label="--p-trunc-len-r: INTEGER Position at which reverse read sequences should be truncated due to decrease in quality. This truncates the 3' end of the of the input sequences, which will be the bases that were sequenced in the last cycles. Reads that are shorter than this value will be discarded. After this parameter is applied there must still be at least a 20 nucleotide overlap between the forward and reverse reads. If 0 is provided, no truncation or length filtering will be performed [required]" name="ptrunclenr" optional="False" value="" type="integer"/> 140 <param label="--p-trunc-len-r: INTEGER Position at which reverse read sequences should be truncated due to decrease in quality. This truncates the 3' end of the of the input sequences, which will be the bases that were sequenced in the last cycles. Reads that are shorter than this value will be discarded. After this parameter is applied there must still be at least a 20 nucleotide overlap between the forward and reverse reads. If 0 is provided, no truncation or length filtering will be performed [required]" name="ptrunclenr" optional="False" value="" type="integer"/>
131 <param label="--p-trim-left-f: INTEGER Position at which forward read sequences should be trimmed due to low quality. This trims the 5' end of the input sequences, which will be the bases that were sequenced in the first cycles. [default: 0]" name="ptrimleftf" optional="True" type="integer" value="0"/> 141 <param label="--p-trim-left-f: INTEGER Position at which forward read sequences should be trimmed due to low quality. This trims the 5' end of the input sequences, which will be the bases that were sequenced in the first cycles. [default: 0]" name="ptrimleftf" optional="True" type="integer" value="0"/>
132 <param label="--p-trim-left-r: INTEGER Position at which reverse read sequences should be trimmed due to low quality. This trims the 5' end of the input sequences, which will be the bases that were sequenced in the first cycles. [default: 0]" name="ptrimleftr" optional="True" type="integer" value="0"/> 142 <param label="--p-trim-left-r: INTEGER Position at which reverse read sequences should be trimmed due to low quality. This trims the 5' end of the input sequences, which will be the bases that were sequenced in the first cycles. [default: 0]" name="ptrimleftr" optional="True" type="integer" value="0"/>
133 <param label="--p-max-ee: NUMBER Reads with number of expected errors higher than this value will be discarded. [default: 2.0]" name="pmaxee" optional="True" type="float" value="2.0"/> 143
144
145
146 <param label="--p-max-ee-f: NUMBER Forward reads with number of expected errors higher than this value will be discarded. [default: 2.0]" name="pmaxeef" optional="True" type="float" value="2.0"/>
147 <param label="--p-max-ee-r: NUMBER Reverse reads with number of expected errors higher than this value will be discarded. [default: 2.0]" name="pmaxeer" optional="True" type="float" value="2.0"/>
148
149
150
134 <param label="--p-trunc-q: INTEGER Reads are truncated at the first instance of a quality score less than or equal to this value. If the resulting read is then shorter than `trunc-len-f` or `trunc-len-r` (depending on the direction of the read) it is discarded. [default: 2]" name="ptruncq" optional="True" type="integer" value="2"/> 151 <param label="--p-trunc-q: INTEGER Reads are truncated at the first instance of a quality score less than or equal to this value. If the resulting read is then shorter than `trunc-len-f` or `trunc-len-r` (depending on the direction of the read) it is discarded. [default: 2]" name="ptruncq" optional="True" type="integer" value="2"/>
135 <param label="--p-chimera-method: " name="pchimeramethod" optional="True" type="select"> 152 <param label="--p-chimera-method: " name="pchimeramethod" optional="True" type="select">
136 <option selected="True" value="None">Selection is Optional</option> 153 <option selected="True" value="None">Selection is Optional</option>
137 <option value="consensus">consensus</option> 154 <option value="consensus">consensus</option>
138 <option value="pooled">pooled</option> 155 <option value="pooled">pooled</option>
147 <data format="qza" label="${tool.name} on ${on_string}: representativesequences.qza" name="orepresentativesequences"/> 164 <data format="qza" label="${tool.name} on ${on_string}: representativesequences.qza" name="orepresentativesequences"/>
148 <data format="qza" label="${tool.name} on ${on_string}: denoisingstats.qza" name="odenoisingstats"/> 165 <data format="qza" label="${tool.name} on ${on_string}: denoisingstats.qza" name="odenoisingstats"/>
149 </outputs> 166 </outputs>
150 <help><![CDATA[ 167 <help><![CDATA[
151 Denoise and dereplicate paired-end sequences 168 Denoise and dereplicate paired-end sequences
152 ############################################ 169 #############################################
153 170
154 This method denoises paired-end sequences, dereplicates them, and filters 171 This method denoises paired-end sequences, dereplicates them, and filters
155 chimeras. 172 chimeras.
156 173
157 Parameters 174 Parameters
180 the bases that were sequenced in the first cycles. 197 the bases that were sequenced in the first cycles.
181 trim_left_r : Int, optional 198 trim_left_r : Int, optional
182 Position at which reverse read sequences should be trimmed due to low 199 Position at which reverse read sequences should be trimmed due to low
183 quality. This trims the 5' end of the input sequences, which will be 200 quality. This trims the 5' end of the input sequences, which will be
184 the bases that were sequenced in the first cycles. 201 the bases that were sequenced in the first cycles.
185 max_ee : Float, optional 202 max_ee_f : Float, optional
186 Reads with number of expected errors higher than this value will be 203 Forward reads with number of expected errors higher than this value
187 discarded. 204 will be discarded.
205 max_ee_r : Float, optional
206 Reverse reads with number of expected errors higher than this value
207 will be discarded.
188 trunc_q : Int, optional 208 trunc_q : Int, optional
189 Reads are truncated at the first instance of a quality score less than 209 Reads are truncated at the first instance of a quality score less than
190 or equal to this value. If the resulting read is then shorter than 210 or equal to this value. If the resulting read is then shorter than
191 `trunc_len_f` or `trunc_len_r` (depending on the direction of the read) 211 `trunc_len_f` or `trunc_len_r` (depending on the direction of the read)
192 it is discarded. 212 it is discarded.
193 chimera_method : Str % Choices('consensus', 'pooled', 'none'), optional 213 chimera_method : Str % Choices('consensus', 'none', 'pooled'), optional
194 The method used to remove chimeras. "none": No chimera removal is 214 The method used to remove chimeras. "none": No chimera removal is
195 performed. "pooled": All reads are pooled prior to chimera detection. 215 performed. "pooled": All reads are pooled prior to chimera detection.
196 "consensus": Chimeras are detected in samples individually, and 216 "consensus": Chimeras are detected in samples individually, and
197 sequences found chimeric in a sufficient fraction of samples are 217 sequences found chimeric in a sufficient fraction of samples are
198 removed. 218 removed.
200 The minimum abundance of potential parents of a sequence being tested 220 The minimum abundance of potential parents of a sequence being tested
201 as chimeric, expressed as a fold-change versus the abundance of the 221 as chimeric, expressed as a fold-change versus the abundance of the
202 sequence being tested. Values should be greater than or equal to 1 222 sequence being tested. Values should be greater than or equal to 1
203 (i.e. parents should be more abundant than the sequence being tested). 223 (i.e. parents should be more abundant than the sequence being tested).
204 This parameter has no effect if chimera_method is "none". 224 This parameter has no effect if chimera_method is "none".
205 provided, all available cores will be used.
206 n_reads_learn : Int, optional 225 n_reads_learn : Int, optional
207 The number of reads to use when training the error model. Smaller 226 The number of reads to use when training the error model. Smaller
208 numbers will result in a shorter run time but a less reliable error 227 numbers will result in a shorter run time but a less reliable error
209 model. 228 model.
210 hashed_feature_ids : Bool, optional 229 hashed_feature_ids : Bool, optional