Mercurial > repos > florianbegusch > qiime2_suite
comparison qiime2-2020.8/qiime_quality-control_exclude-seqs.xml @ 20:d93d8888f0b0 draft
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author | florianbegusch |
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date | Fri, 04 Sep 2020 12:44:24 +0000 |
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19:6c48f8d82424 | 20:d93d8888f0b0 |
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1 <?xml version="1.0" ?> | |
2 <tool id="qiime_quality-control_exclude-seqs" name="qiime quality-control exclude-seqs" | |
3 version="2020.8"> | |
4 <description>Exclude sequences by alignment</description> | |
5 <requirements> | |
6 <requirement type="package" version="2020.8">qiime2</requirement> | |
7 </requirements> | |
8 <command><![CDATA[ | |
9 qiime quality-control exclude-seqs | |
10 | |
11 --i-query-sequences=$iquerysequences | |
12 | |
13 --i-reference-sequences=$ireferencesequences | |
14 | |
15 #if str($pmethod) != 'None': | |
16 --p-method=$pmethod | |
17 #end if | |
18 | |
19 --p-perc-identity=$ppercidentity | |
20 | |
21 #if str($pevalue): | |
22 --p-evalue=$pevalue | |
23 #end if | |
24 --p-perc-query-aligned=$ppercqueryaligned | |
25 | |
26 --p-threads=$pthreads | |
27 | |
28 #if str($pleftjustify) != 'None': | |
29 --p-left-justify=$pleftjustify | |
30 #end if | |
31 | |
32 --o-sequence-hits=osequencehits | |
33 | |
34 --o-sequence-misses=osequencemisses | |
35 | |
36 #if str($examples) != 'None': | |
37 --examples=$examples | |
38 #end if | |
39 | |
40 ; | |
41 cp osequencemisses.qza $osequencemisses | |
42 | |
43 ]]></command> | |
44 <inputs> | |
45 <param format="qza,no_unzip.zip" label="--i-query-sequences: ARTIFACT FeatureData[Sequence] Sequences to test for exclusion [required]" name="iquerysequences" optional="False" type="data" /> | |
46 <param format="qza,no_unzip.zip" label="--i-reference-sequences: ARTIFACT FeatureData[Sequence] Reference sequences to align against feature sequences [required]" name="ireferencesequences" optional="False" type="data" /> | |
47 <param label="--p-method: " name="pmethod" optional="True" type="select"> | |
48 <option selected="True" value="None">Selection is Optional</option> | |
49 <option value="blast">blast</option> | |
50 <option value="blastn-short">blastn-short</option> | |
51 </param> | |
52 <param exclude_max="False" label="--p-perc-identity: PROPORTION Range(0.0, 1.0, inclusive_end=True) Reject match if percent identity to reference is lower. Must be in range [0.0, 1.0] [default: 0.97]" max="1.0" min="0.0" name="ppercidentity" optional="True" type="float" value="0.97" /> | |
53 <param label="--p-evalue: NUMBER BLAST expectation (E) value threshold for saving hits. Reject if E value is higher than threshold. This threshold is disabled by default. [optional]" name="pevalue" optional="False" type="text" /> | |
54 <param label="--p-perc-query-aligned: NUMBER Percent of query sequence that must align to reference in order to be accepted as a hit. [default: 0.97]" name="ppercqueryaligned" optional="True" type="float" value="0.97" /> | |
55 <param label="--p-left-justify: " name="pleftjustify" optional="True" type="select"> | |
56 <option selected="True" value="None">Selection is Optional</option> | |
57 <option value="False">False</option> | |
58 </param> | |
59 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" /> | |
60 | |
61 </inputs> | |
62 | |
63 <outputs> | |
64 <data format="qza" label="${tool.name} on ${on_string}: sequencehits.qza" name="osequencehits" /> | |
65 <data format="qza" label="${tool.name} on ${on_string}: sequencemisses.qza" name="osequencemisses" /> | |
66 | |
67 </outputs> | |
68 | |
69 <help><![CDATA[ | |
70 Exclude sequences by alignment | |
71 ############################################################### | |
72 | |
73 This method aligns feature sequences to a set of reference sequences to | |
74 identify sequences that hit/miss the reference within a specified | |
75 perc_identity, evalue, and perc_query_aligned. This method could be used to | |
76 define a positive filter, e.g., extract only feature sequences that align | |
77 to a certain clade of bacteria; or to define a negative filter, e.g., | |
78 identify sequences that align to contaminant or human DNA sequences that | |
79 should be excluded from subsequent analyses. Note that filtering is | |
80 performed based on the perc_identity, perc_query_aligned, and evalue | |
81 thresholds (the latter only if method==BLAST and an evalue is set). Set | |
82 perc_identity==0 and/or perc_query_aligned==0 to disable these filtering | |
83 thresholds as necessary. | |
84 | |
85 Parameters | |
86 ---------- | |
87 query_sequences : FeatureData[Sequence] | |
88 Sequences to test for exclusion | |
89 reference_sequences : FeatureData[Sequence] | |
90 Reference sequences to align against feature sequences | |
91 method : Str % Choices('blast', 'blastn-short')¹ | Str % Choices('vsearch')², optional | |
92 Alignment method to use for matching feature sequences against | |
93 reference sequences | |
94 perc_identity : Float % Range(0.0, 1.0, inclusive_end=True), optional | |
95 Reject match if percent identity to reference is lower. Must be in | |
96 range [0.0, 1.0] | |
97 evalue : Float, optional | |
98 BLAST expectation (E) value threshold for saving hits. Reject if E | |
99 value is higher than threshold. This threshold is disabled by default. | |
100 perc_query_aligned : Float, optional | |
101 Percent of query sequence that must align to reference in order to be | |
102 accepted as a hit. | |
103 threads : Int % Range(1, None), optional | |
104 Number of jobs to execute. Only applies to vsearch method. | |
105 left_justify : Bool % Choices(False)¹ | Bool², optional | |
106 Reject match if the pairwise alignment begins with gaps | |
107 | |
108 Returns | |
109 ------- | |
110 sequence_hits : FeatureData[Sequence] | |
111 Subset of feature sequences that align to reference sequences | |
112 sequence_misses : FeatureData[Sequence] | |
113 Subset of feature sequences that do not align to reference sequences | |
114 ]]></help> | |
115 <macros> | |
116 <import>qiime_citation.xml</import> | |
117 </macros> | |
118 <expand macro="qiime_citation"/> | |
119 </tool> |