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comparison qiime2/qiime_quality-control_exclude-seqs.xml @ 0:370e0b6e9826 draft

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author florianbegusch
date Wed, 17 Jul 2019 03:05:17 -0400
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1 <?xml version="1.0" ?>
2 <tool id="qiime_quality-control_exclude-seqs" name="qiime quality-control exclude-seqs" version="2019.4">
3 <description> - Exclude sequences by alignment</description>
4 <requirements>
5 <requirement type="package" version="2019.4">qiime2</requirement>
6 </requirements>
7 <command><![CDATA[
8 qiime quality-control exclude-seqs
9
10 --i-query-sequences=$iquerysequences
11 --i-reference-sequences=$ireferencesequences
12
13 #if str($pmethod) != 'None':
14 --p-method=$pmethod
15 #end if
16
17 #if $ppercidentity:
18 --p-perc-identity=$ppercidentity
19 #end if
20
21 #if str($pevalue):
22 --p-evalue="$pevalue"
23 #end if
24
25 #if $ppercqueryaligned:
26 --p-perc-query-aligned=$ppercqueryaligned
27 #end if
28
29 #set $pthreads = '${GALAXY_SLOTS:-4}'
30 #if str($pthreads):
31 --p-threads="$pthreads"
32 #end if
33
34 --o-sequence-hits=osequencehits
35 --o-sequence-misses=osequencemisses
36 ;
37 cp osequencehits.qza $osequencehits;
38 cp osequencemisses.qza $osequencemisses
39 ]]></command>
40 <inputs>
41 <param format="qza,no_unzip.zip" label="--i-query-sequences: ARTIFACT FeatureData[Sequence] Sequences to test for exclusion [required]" name="iquerysequences" optional="False" type="data"/>
42 <param format="qza,no_unzip.zip" label="--i-reference-sequences: ARTIFACT FeatureData[Sequence] Reference sequences to align against feature sequences [required]" name="ireferencesequences" optional="False" type="data"/>
43 <param label="--p-method: " name="pmethod" optional="True" type="select">
44 <option selected="True" value="None">Selection is Optional</option>
45 <option value="blast">blast</option>
46 <option value="vsearch">vsearch</option>
47 <option value="blastn-short">blastn-short</option>
48 </param>
49 <param label="--p-perc-identity: PROPORTION Range(0.0, 1.0, inclusive_end=True) Reject match if percent identity to reference is lower. Must be in range [0.0, 1.0] [default: 0.97]" name="ppercidentity" optional="True" type="float" value="0.97" min="0" max="1" exclusive_end="False"/>
50 <param label="--p-evalue: NUMBER BLAST expectation (E) value threshold for saving hits. Reject if E value is higher than threshold. This threshold is disabled by default. [optional]" name="pevalue" optional="True" type="text"/>
51 <param label="--p-perc-query-aligned: NUMBER Percent of query sequence that must align to reference in order to be accepted as a hit. [default: 0.97]" name="ppercqueryaligned" optional="True" type="float" value="0.97"/>
52 </inputs>
53 <outputs>
54 <data format="qza" label="${tool.name} on ${on_string}: sequencehits.qza" name="osequencehits"/>
55 <data format="qza" label="${tool.name} on ${on_string}: sequencemisses.qza" name="osequencemisses"/>
56 </outputs>
57 <help><![CDATA[
58 Exclude sequences by alignment
59 ##############################
60
61 This method aligns feature sequences to a set of reference sequences to
62 identify sequences that hit/miss the reference within a specified
63 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
65 to a certain clade of bacteria; or to define a negative filter, e.g.,
66 identify sequences that align to contaminant or human DNA sequences that
67 should be excluded from subsequent analyses. Note that filtering is
68 performed based on the perc_identity, perc_query_aligned, and evalue
69 thresholds (the latter only if method==BLAST and an evalue is set). Set
70 perc_identity==0 and/or perc_query_aligned==0 to disable these filtering
71 thresholds as necessary.
72
73 Parameters
74 ----------
75 query_sequences : FeatureData[Sequence]
76 Sequences to test for exclusion
77 reference_sequences : FeatureData[Sequence]
78 Reference sequences to align against feature sequences
79 method : Str % Choices('blast', 'vsearch', 'blastn-short'), optional
80 Alignment method to use for matching feature sequences against
81 reference sequences
82 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
84 range [0.0, 1.0]
85 evalue : Float, optional
86 BLAST expectation (E) value threshold for saving hits. Reject if E
87 value is higher than threshold. This threshold is disabled by default.
88 perc_query_aligned : Float, optional
89 Percent of query sequence that must align to reference in order to be
90 accepted as a hit.
91
92 Returns
93 -------
94 sequence_hits : FeatureData[Sequence]
95 Subset of feature sequences that align to reference sequences
96 sequence_misses : FeatureData[Sequence]
97 Subset of feature sequences that do not align to reference sequences
98 ]]></help>
99 <macros>
100 <import>qiime_citation.xml</import>
101 </macros>
102 <expand macro="qiime_citation"/>
103 </tool>