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comparison qiime2/qiime_quality-control_exclude-seqs.xml @ 14:a0a8d77a991c draft

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author florianbegusch
date Thu, 03 Sep 2020 09:51:29 +0000
parents f190567fe3f6
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13:887cd4ad8e16 14:a0a8d77a991c
1 <?xml version="1.0" ?> 1 <?xml version="1.0" ?>
2 <tool id="qiime_quality-control_exclude-seqs" name="qiime quality-control exclude-seqs" version="2019.7"> 2 <tool id="qiime_quality-control_exclude-seqs" name="qiime quality-control exclude-seqs"
3 <description> - Exclude sequences by alignment</description> 3 version="2020.8">
4 <requirements> 4 <description>Exclude sequences by alignment</description>
5 <requirement type="package" version="2019.7">qiime2</requirement> 5 <requirements>
6 </requirements> 6 <requirement type="package" version="2020.8">qiime2</requirement>
7 <command><![CDATA[ 7 </requirements>
8 <command><![CDATA[
8 qiime quality-control exclude-seqs 9 qiime quality-control exclude-seqs
9 10
10 --i-query-sequences=$iquerysequences 11 --i-query-sequences=$iquerysequences
12
11 --i-reference-sequences=$ireferencesequences 13 --i-reference-sequences=$ireferencesequences
12 14
13 #if str($pmethod) != 'None': 15 #if str($pmethod) != 'None':
14 --p-method=$pmethod 16 --p-method=$pmethod
15 #end if 17 #end if
16 18
17 #if str($ppercidentity): 19 --p-perc-identity=$ppercidentity
18 --p-perc-identity=$ppercidentity
19 #end if
20 20
21 #if str($pevalue): 21 #if str($pevalue):
22 --p-evalue="$pevalue" 22 --p-evalue=$pevalue
23 #end if 23 #end if
24 --p-perc-query-aligned=$ppercqueryaligned
24 25
25 #if str($ppercqueryaligned): 26 --p-threads=$pthreads
26 --p-perc-query-aligned=$ppercqueryaligned
27 #end if
28 27
29 #set $pthreads = '${GALAXY_SLOTS:-4}' 28 #if str($pleftjustify) != 'None':
30 #if str($pthreads): 29 --p-left-justify=$pleftjustify
31 --p-threads="$pthreads"
32 #end if 30 #end if
33 31
34 --o-sequence-hits=osequencehits 32 --o-sequence-hits=osequencehits
33
35 --o-sequence-misses=osequencemisses 34 --o-sequence-misses=osequencemisses
35
36 #if str($examples) != 'None':
37 --examples=$examples
38 #end if
39
36 ; 40 ;
37 cp osequencehits.qza $osequencehits;
38 cp osequencemisses.qza $osequencemisses 41 cp osequencemisses.qza $osequencemisses
39 ]]></command> 42
40 <inputs> 43 ]]></command>
41 <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"/> 44 <inputs>
42 <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"/> 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" />
43 <param label="--p-method: " name="pmethod" optional="True" type="select"> 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" />
44 <option selected="True" value="None">Selection is Optional</option> 47 <param label="--p-method: " name="pmethod" optional="True" type="select">
45 <option value="blast">blast</option> 48 <option selected="True" value="None">Selection is Optional</option>
46 <option value="vsearch">vsearch</option> 49 <option value="blast">blast</option>
47 <option value="blastn-short">blastn-short</option> 50 <option value="blastn-short">blastn-short</option>
48 </param> 51 </param>
49 <param 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]" name="ppercidentity" optional="True" type="float" value="0.97" min="0" max="1" exclusive_end="False"/> 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" />
50 <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="True" type="float"/> 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" />
51 <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"/> 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" />
52 </inputs> 55 <param label="--p-left-justify: " name="pleftjustify" optional="True" type="select">
53 <outputs> 56 <option selected="True" value="None">Selection is Optional</option>
54 <data format="qza" label="${tool.name} on ${on_string}: sequencehits.qza" name="osequencehits"/> 57 <option value="False">False</option>
55 <data format="qza" label="${tool.name} on ${on_string}: sequencemisses.qza" name="osequencemisses"/> 58 </param>
56 </outputs> 59 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
57 <help><![CDATA[ 60
61 </inputs>
62
63 <outputs>
64 <data format="qza" label="${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[
58 Exclude sequences by alignment 70 Exclude sequences by alignment
59 ############################## 71 ###############################################################
60 72
61 This method aligns feature sequences to a set of reference sequences to 73 This method aligns feature sequences to a set of reference sequences to
62 identify sequences that hit/miss the reference within a specified 74 identify sequences that hit/miss the reference within a specified
63 perc_identity, evalue, and perc_query_aligned. This method could be used to 75 perc_identity, evalue, and perc_query_aligned. This method could be used to
64 define a positive filter, e.g., extract only feature sequences that align 76 define a positive filter, e.g., extract only feature sequences that align
74 ---------- 86 ----------
75 query_sequences : FeatureData[Sequence] 87 query_sequences : FeatureData[Sequence]
76 Sequences to test for exclusion 88 Sequences to test for exclusion
77 reference_sequences : FeatureData[Sequence] 89 reference_sequences : FeatureData[Sequence]
78 Reference sequences to align against feature sequences 90 Reference sequences to align against feature sequences
79 method : Str % Choices('blast', 'vsearch', 'blastn-short'), optional 91 method : Str % Choices('blast', 'blastn-short')¹ | Str % Choices('vsearch')², optional
80 Alignment method to use for matching feature sequences against 92 Alignment method to use for matching feature sequences against
81 reference sequences 93 reference sequences
82 perc_identity : Float % Range(0.0, 1.0, inclusive_end=True), optional 94 perc_identity : Float % Range(0.0, 1.0, inclusive_end=True), optional
83 Reject match if percent identity to reference is lower. Must be in 95 Reject match if percent identity to reference is lower. Must be in
84 range [0.0, 1.0] 96 range [0.0, 1.0]
86 BLAST expectation (E) value threshold for saving hits. Reject if E 98 BLAST expectation (E) value threshold for saving hits. Reject if E
87 value is higher than threshold. This threshold is disabled by default. 99 value is higher than threshold. This threshold is disabled by default.
88 perc_query_aligned : Float, optional 100 perc_query_aligned : Float, optional
89 Percent of query sequence that must align to reference in order to be 101 Percent of query sequence that must align to reference in order to be
90 accepted as a hit. 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
91 107
92 Returns 108 Returns
93 ------- 109 -------
94 sequence_hits : FeatureData[Sequence] 110 sequence_hits : FeatureData[Sequence]
95 Subset of feature sequences that align to reference sequences 111 Subset of feature sequences that align to reference sequences
96 sequence_misses : FeatureData[Sequence] 112 sequence_misses : FeatureData[Sequence]
97 Subset of feature sequences that do not align to reference sequences 113 Subset of feature sequences that do not align to reference sequences
98 ]]></help> 114 ]]></help>
99 <macros> 115 <macros>
100 <import>qiime_citation.xml</import> 116 <import>qiime_citation.xml</import>
101 </macros> 117 </macros>
102 <expand macro="qiime_citation"/> 118 <expand macro="qiime_citation"/>
103 </tool> 119 </tool>