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comparison qiime2/qiime_feature-table_filter-seqs.xml @ 0:370e0b6e9826 draft

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author florianbegusch
date Wed, 17 Jul 2019 03:05:17 -0400
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children f190567fe3f6
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-1:000000000000 0:370e0b6e9826
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>