annotate qiime2/qiime_deblur_denoise-other.xml @ 1:255f48db74f8 draft

Hotfix
author florianbegusch
date Wed, 17 Jul 2019 03:26:16 -0400
parents 370e0b6e9826
children de4c22a52df4
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
1 <?xml version="1.0" ?>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
2 <tool id="qiime_deblur_denoise-other" name="qiime deblur denoise-other" version="2019.4">
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
3 <description> - Deblur sequences using a user-specified positive filter.</description>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
4 <requirements>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
5 <requirement type="package" version="2019.4">qiime2</requirement>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
6 </requirements>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
7 <command><![CDATA[
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
8 qiime deblur denoise-other
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
9
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
10 --i-demultiplexed-seqs=$idemultiplexedseqs
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
11 --i-reference-seqs=$ireferenceseqs
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
12 --p-trim-length="$ptrimlength"
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
13
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
14 #if $plefttrimlen:
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
15 --p-left-trim-len=$plefttrimlen
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
16 #end if
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
17
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
18 #if $psamplestats:
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
19 --p-sample-stats
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
20 #end if
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
21
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
22 #if $pmeanerror:
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
23 --p-mean-error=$pmeanerror
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
24 #end if
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
25
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
26 #if $pindelprob:
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
27 --p-indel-prob=$pindelprob
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
28 #end if
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
29
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
30 #if $pindelmax:
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
31 --p-indel-max=$pindelmax
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
32 #end if
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
33
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
34 #if $pminreads:
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
35 --p-min-reads=$pminreads
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
36 #end if
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
37
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
38 #if $pminsize:
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
39 --p-min-size=$pminsize
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
40 #end if
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
41
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
42 #set $pjobstostart = '${GALAXY_SLOTS:-4}'
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
43
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
44 #if str($pjobstostart):
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
45 --p-jobs-to-start="$pjobstostart"
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
46 #end if
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
47
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
48
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
49 #if $pnohashedfeatureids:
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
50 --p-no-hashed-feature-ids
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
51 #end if
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
52
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
53 --o-table=otable
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
54 --o-representative-sequences=orepresentativesequences
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
55 --o-stats=ostats
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
56 ;
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
57 cp otable.qza $otable;
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
58 cp orepresentativesequences.qza $orepresentativesequences;
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
59 cp ostats.qza $ostats
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
60 ]]></command>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
61 <inputs>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
62 <param format="qza,no_unzip.zip" label="--i-demultiplexed-seqs: ARTIFACT SampleData[SequencesWithQuality | PairedEndSequencesWithQuality | JoinedSequencesWithQuality] The demultiplexed sequences to be denoised. [required]" name="idemultiplexedseqs" optional="False" type="data"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
63 <param format="qza,no_unzip.zip" label="--i-reference-seqs: ARTIFACT FeatureData[Sequence] Positive filtering database. Keep all sequences aligning to these sequences. [required]" name="ireferenceseqs" optional="False" type="data"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
64 <param label="--p-trim-length: INTEGER Sequence trim length, specify -1 to disable trimming. [required]" name="ptrimlength" optional="False" value="" type="integer"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
65 <param label="--p-left-trim-len: INTEGER Range(0, None) Sequence trimming from the 5' end. A value of 0 will disable this trim. [default: 0]" name="plefttrimlen" optional="True" type="integer" min="0" value="0"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
66 <param label="--p-sample-stats: --p-no-sample-stats If true, gather stats per sample. [default: False]" name="psamplestats" selected="False" type="boolean"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
67 <param label="--p-mean-error: NUMBER The mean per nucleotide error, used for original sequence estimate. [default: 0.005]" name="pmeanerror" optional="True" type="float" value="0.005"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
68 <param label="--p-indel-prob: NUMBER Insertion/deletion (indel) probability (same for N indels). [default: 0.01]" name="pindelprob" optional="True" type="float" value="0.01"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
69 <param label="--p-indel-max: INTEGER Maximum number of insertion/deletions. [default: 3]" name="pindelmax" optional="True" type="integer" value="3"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
70 <param label="--p-min-reads: INTEGER Retain only features appearing at least min-reads times across all samples in the resulting feature table. [default: 10]" name="pminreads" optional="True" type="integer" value="10"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
71 <param label="--p-min-size: INTEGER In each sample, discard all features with an abundance less than min-size. [default: 2]" name="pminsize" optional="True" type="integer" value="2"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
72 <param label="--p-no-hashed-feature-ids: If false, hash the feature IDs. [default: False]" name="pnohashedfeatureids" selected="False" type="boolean"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
73 </inputs>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
74 <outputs>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
75 <data format="qza" label="${tool.name} on ${on_string}: table.qza" name="otable"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
76 <data format="qza" label="${tool.name} on ${on_string}: representativesequences.qza" name="orepresentativesequences"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
77 <data format="qza" label="${tool.name} on ${on_string}: stats.qza" name="ostats"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
78 </outputs>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
79 <help><![CDATA[
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
80 Deblur sequences using a user-specified positive filter.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
81 ########################################################
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
82
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
83 Perform sequence quality control for Illumina data using the Deblur
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
84 workflow, including positive alignment-based filtering. Only forward reads
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
85 are supported at this time. This mode of execution is particularly useful
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
86 when operating on non-16S data. For example, to apply Deblur to 18S data,
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
87 you would want to specify a reference composed of 18S sequences in order to
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
88 filter out sequences which do not appear to be 18S. The assessment is
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
89 performed by local alignment using SortMeRNA with a permissive e-value
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
90 threshold.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
91
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
92 Parameters
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
93 ----------
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
94 demultiplexed_seqs : SampleData[SequencesWithQuality | PairedEndSequencesWithQuality | JoinedSequencesWithQuality]
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
95 The demultiplexed sequences to be denoised.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
96 reference_seqs : FeatureData[Sequence]
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
97 Positive filtering database. Keep all sequences aligning to these
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
98 sequences.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
99 trim_length : Int
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
100 Sequence trim length, specify -1 to disable trimming.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
101 left_trim_len : Int % Range(0, None), optional
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
102 Sequence trimming from the 5' end. A value of 0 will disable this trim.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
103 sample_stats : Bool, optional
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
104 If true, gather stats per sample.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
105 mean_error : Float, optional
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
106 The mean per nucleotide error, used for original sequence estimate.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
107 indel_prob : Float, optional
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
108 Insertion/deletion (indel) probability (same for N indels).
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
109 indel_max : Int, optional
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
110 Maximum number of insertion/deletions.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
111 min_reads : Int, optional
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
112 Retain only features appearing at least min_reads times across all
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
113 samples in the resulting feature table.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
114 min_size : Int, optional
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
115 In each sample, discard all features with an abundance less than
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
116 min_size.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
117 hashed_feature_ids : Bool, optional
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
118 If true, hash the feature IDs.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
119
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
120 Returns
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
121 -------
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
122 table : FeatureTable[Frequency]
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
123 The resulting denoised feature table.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
124 representative_sequences : FeatureData[Sequence]
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
125 The resulting feature sequences.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
126 stats : DeblurStats
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
127 Per-sample stats if requested.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
128 ]]></help>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
129 <macros>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
130 <import>qiime_citation.xml</import>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
131 </macros>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
132 <expand macro="qiime_citation"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
133 </tool>