0
|
1 <?xml version="1.0" ?>
|
|
2 <tool id="qiime_feature-table_filter-seqs" name="qiime feature-table filter-seqs" version="2019.4">
|
|
3 <description> - Filter features from sequences</description>
|
|
4 <requirements>
|
|
5 <requirement type="package" version="2019.4">qiime2</requirement>
|
|
6 </requirements>
|
|
7 <command><![CDATA[
|
|
8 qiime feature-table filter-seqs
|
|
9
|
|
10 --i-data=$idata
|
|
11
|
|
12
|
|
13 #if $input_files_mmetadatafile:
|
|
14 #def list_dict_to_string(list_dict):
|
|
15 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
|
|
16 #for d in list_dict[1:]:
|
|
17 #set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
|
|
18 #end for
|
|
19 #return $file_list
|
|
20 #end def
|
|
21 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
|
|
22 #end if
|
|
23
|
|
24
|
|
25 #if str($itable) != 'None':
|
|
26 --i-table=$itable
|
|
27 #end if
|
|
28
|
|
29 #if '__sq__' in str($pwhere):
|
|
30 #set $pwhere_temp = $pwhere.replace('__sq__', "'")
|
|
31 #set $pwhere = $pwhere_temp
|
|
32 #end if
|
|
33
|
|
34 #if str($pwhere):
|
|
35 --p-where="$pwhere"
|
|
36 #end if
|
|
37
|
|
38 #if $pexcludeids:
|
|
39 --p-exclude-ids
|
|
40 #end if
|
|
41
|
|
42 --o-filtered-data=ofiltereddata
|
|
43 ;
|
|
44 cp ofiltereddata.qza $ofiltereddata
|
|
45 ]]></command>
|
|
46 <inputs>
|
|
47 <param format="qza,no_unzip.zip" label="--i-data: ARTIFACT FeatureData[Sequence] The sequences from which features should be filtered. [required]" name="idata" optional="False" type="data"/>
|
|
48 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] Table containing feature ids used for id-based filtering. [optional]" name="itable" optional="True" type="data"/>
|
|
49 <param label="--p-where: TEXT SQLite WHERE clause specifying feature metadata criteria that must be met to be included in the filtered feature table. If not provided, all features in `metadata` that are also in the sequences will be retained. [optional]" name="pwhere" optional="True" type="text"/>
|
|
50 <param label="--p-exclude-ids: --p-no-exclude-ids If true, the features selected by the `metadata` (with or without the `where` parameter) or `table` parameter will be excluded from the filtered sequences instead of being retained. [default: False]" name="pexcludeids" selected="False" type="boolean"/>
|
|
51
|
|
52 <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file">
|
|
53 <param label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [optional]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
|
|
54 </repeat>
|
|
55
|
|
56 </inputs>
|
|
57 <outputs>
|
|
58 <data format="qza" label="${tool.name} on ${on_string}: filtereddata.qza" name="ofiltereddata"/>
|
|
59 </outputs>
|
|
60 <help><![CDATA[
|
|
61 Filter features from sequences
|
|
62 ##############################
|
|
63
|
|
64 Filter features from sequences based on a feature table or metadata. See
|
|
65 the filtering tutorial on https://docs.qiime2.org for additional details.
|
|
66 This method can filter based on ids in a table or a metadata file, but not
|
|
67 both (i.e., the table and metadata options are mutually exclusive).
|
|
68
|
|
69 Parameters
|
|
70 ----------
|
|
71 data : FeatureData[Sequence]
|
|
72 The sequences from which features should be filtered.
|
|
73 table : FeatureTable[Frequency], optional
|
|
74 Table containing feature ids used for id-based filtering.
|
|
75 metadata : Metadata, optional
|
|
76 Feature metadata used for id-based filtering, with `where` parameter
|
|
77 when selecting features to retain, or with `exclude_ids` when selecting
|
|
78 features to discard.
|
|
79 where : Str, optional
|
|
80 SQLite WHERE clause specifying feature metadata criteria that must be
|
|
81 met to be included in the filtered feature table. If not provided, all
|
|
82 features in `metadata` that are also in the sequences will be retained.
|
|
83 exclude_ids : Bool, optional
|
|
84 If true, the features selected by the `metadata` (with or without the
|
|
85 `where` parameter) or `table` parameter will be excluded from the
|
|
86 filtered sequences instead of being retained.
|
|
87
|
|
88 Returns
|
|
89 -------
|
|
90 filtered_data : FeatureData[Sequence]
|
|
91 The resulting filtered sequences.
|
|
92 ]]></help>
|
|
93 <macros>
|
|
94 <import>qiime_citation.xml</import>
|
|
95 </macros>
|
|
96 <expand macro="qiime_citation"/>
|
|
97 </tool>
|