Mercurial > repos > florianbegusch > qiime2_wrappers

comparison qiime2/qiime_quality-control_exclude-seqs.xml @ 0:51b9b6b57732 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author florianbegusch
date Thu, 24 May 2018 05:21:07 -0400
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:51b9b6b57732
1 <?xml version="1.0" ?>
2 <tool id="qiime_quality-control_exclude-seqs" name="qiime quality-control exclude-seqs" version="2018.4">
3 <description> - Exclude sequences by alignment</description>
4 <requirements>
5 <requirement type="package" version="2018.4">qiime2</requirement>
6 </requirements>
7 <command>
8 <![CDATA[
9 qiime quality-control exclude-seqs --i-reference-sequences=$ireferencesequences --i-query-sequences=$iquerysequences
10 #if str($pevalue):
11 --p-evalue="$pevalue"
12 #end if
13
14 #if $ppercidentity:
15 --p-perc-identity=$ppercidentity
16 #end if
17
18 #if $ppercqueryaligned:
19 --p-perc-query-aligned=$ppercqueryaligned
20 #end if
21
22 #if str($cmdconfig) != 'None':
23 --cmd-config=$cmdconfig
24 #end if
25 --o-sequence-hits=osequencehits --o-sequence-misses=osequencemisses
26 #if str($pmethod) != 'None':
27 --p-method=$pmethod
28 #end if
29
30 #set $pthreads = '${GALAXY_SLOTS:-4}'
31
32 #if str($pthreads):
33 --p-threads="$pthreads"
34 #end if
35 ;
36 cp osequencehits.qza $osequencehits;
37 cp osequencemisses.qza $osequencemisses;
38 ]]>
39 </command>
40 <inputs>
41 <param format="qza,no_unzip.zip" label="--i-query-sequences: FeatureData[Sequence] Sequences to test for exclusion [required]" name="iquerysequences" optional="False" type="data"/>
42 <param format="qza,no_unzip.zip" label="--i-reference-sequences: FeatureData[Sequence] Reference sequences to align against feature sequences [required]" name="ireferencesequences" optional="False" type="data"/>
43
44 <param label="--p-method: Alignment method to use for matching feature
45 sequences against reference sequences
46 [default: blast]" name="pmethod" optional="True" type="select">
47 <option selected="True" value="None">Selection is Optional</option>
48 <option value="vsearch">vsearch</option>
49 <option value="blast">blast</option>
50 <option value="blastn-short">blastn-short</option>
51 </param>
52
53 <param label="--p-perc-identity: Reject match if percent identity to reference is lower. Must be in range [0.0, 1.0] [default: 0.97]" name="ppercidentity" optional="True" type="float" value="0.97"/>
54 <param label="--p-evalue: BLAST expectation (E) value threshold for saving hits. Reject if E value is higher than threshold. This threshold is disabled by default. [optional]" name="pevalue" optional="True" type="text"/>
55 <param label="--p-perc-query-aligned: Percent of query sequence that must align to reference in order to be accepted as a hit. [default: 0.97]" name="ppercqueryaligned" optional="True" type="float" value="0.97"/>
56
57 <param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
58 </inputs>
59 <outputs>
60 <data format="qza" label="${tool.name} on ${on_string}: sequence-hits.qza" name="osequencehits"/>
61 <data format="qza" label="${tool.name} on ${on_string}: sequence-misses.qza" name="osequencemisses"/>
62 </outputs>
63 <help><![CDATA[
64 Exclude sequences by alignment
65 -------------------------------
66
67 This method aligns feature sequences to a set of reference sequences to
68 identify sequences that hit/miss the reference within a specified
69 perc_identity, evalue, and perc_query_aligned. This method could be used to
70 define a positive filter, e.g., extract only feature sequences that align
71 to a certain clade of bacteria; or to define a negative filter, e.g.,
72 identify sequences that align to contaminant or human DNA sequences that
73 should be excluded from subsequent analyses. Note that filtering is
74 performed based on the perc_identity, perc_query_aligned, and evalue
75 thresholds (the latter only if method==BLAST and an evalue is set). Set
76 perc_identity==0 and/or perc_query_aligned==0 to disable these filtering
77 thresholds as necessary.
78
79 Parameters
80 ----------
81 query_sequences : FeatureData[Sequence]
82 Sequences to test for exclusion
83 reference_sequences : FeatureData[Sequence]
84 Reference sequences to align against feature sequences
85 method : Str % Choices({'blast', 'blastn-short', 'vsearch'}), optional
86 Alignment method to use for matching feature sequences against
87 reference sequences
88 perc_identity : Float % Range(0.0, 1.0, inclusive_end=True), optional
89 Reject match if percent identity to reference is lower. Must be in
90 range [0.0, 1.0]
91 evalue : Float, optional
92 BLAST expectation (E) value threshold for saving hits. Reject if E
93 value is higher than threshold. This threshold is disabled by default.
94 perc_query_aligned : Float, optional
95 Percent of query sequence that must align to reference in order to be
96 accepted as a hit.
97
98 Returns
99 -------
100 sequence_hits : FeatureData[Sequence]
101 Subset of feature sequences that align to reference sequences
102 sequence_misses : FeatureData[Sequence]
103 Subset of feature sequences that do not align to reference sequences
104 ]]>
105 </help>
106 <macros>
107 <import>qiime_citation.xml</import>
108 </macros>
109 <expand macro="qiime_citation" />
110 </tool>