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comparison qiime2/qiime_feature-table_filter-seqs.xml @ 29:3ba9833030c1 draft

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author florianbegusch
date Fri, 04 Sep 2020 13:12:49 +0000
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28:c28331a63dfd 29:3ba9833030c1
1 <?xml version="1.0" ?>
2 <tool id="qiime_feature-table_filter-seqs" name="qiime feature-table filter-seqs"
3 version="2020.8">
4 <description>Filter features from sequences</description>
5 <requirements>
6 <requirement type="package" version="2020.8">qiime2</requirement>
7 </requirements>
8 <command><![CDATA[
9 qiime feature-table filter-seqs
10 # if $input_files_idata:
11 # def list_dict_to_string(list_dict):
12 # set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
13 # for d in list_dict[1:]:
14 # set $file_list = $file_list + ' --i-data=' + d['additional_input'].__getattr__('file_name')
15 # end for
16 # return $file_list
17 # end def
18 --i-data=$list_dict_to_string($input_files_idata)
19 # end if
20
21 #if str($itable) != 'None':
22 --i-table=$itable
23 #end if
24 # if $input_files_mmetadatafile:
25 # def list_dict_to_string(list_dict):
26 # set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
27 # for d in list_dict[1:]:
28 # set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
29 # end for
30 # return $file_list
31 # end def
32 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
33 # end if
34
35 #if '__ob__' in str($pwhere):
36 #set $pwhere_temp = $pwhere.replace('__ob__', '[')
37 #set $pwhere = $pwhere_temp
38 #end if
39 #if '__cb__' in str($pwhere):
40 #set $pwhere_temp = $pwhere.replace('__cb__', ']')
41 #set $pwhere = $pwhere_temp
42 #end if
43 #if 'X' in str($pwhere):
44 #set $pwhere_temp = $pwhere.replace('X', '\\')
45 #set $pwhere = $pwhere_temp
46 #end if
47 #if '__sq__' in str($pwhere):
48 #set $pwhere_temp = $pwhere.replace('__sq__', "'")
49 #set $pwhere = $pwhere_temp
50 #end if
51 #if '__db__' in str($pwhere):
52 #set $pwhere_temp = $pwhere.replace('__db__', '"')
53 #set $pwhere = $pwhere_temp
54 #end if
55
56 #if str($pwhere):
57 --p-where=$pwhere
58 #end if
59
60 #if $pexcludeids:
61 --p-exclude-ids
62 #end if
63
64 --o-filtered-data=ofiltereddata
65
66 #if str($examples) != 'None':
67 --examples=$examples
68 #end if
69
70 ;
71 cp ofiltereddata.qza $ofiltereddata
72
73 ]]></command>
74 <inputs>
75 <repeat name="input_files_idata" optional="False" title="--i-data">
76 <param format="qza,no_unzip.zip" label="--i-data: ARTIFACT FeatureData[Sequence¹ | AlignedSequence²] The sequences from which features should be filtered. [required]" name="additional_input" optional="False" type="data" />
77 </repeat>
78 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] Table containing feature ids used for id-based filtering. [optional]" name="itable" optional="False" type="data" />
79 <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file">
80 <param format="tabular,qza,no_unzip.zip" label="--m-metadata-file: METADATA... (multiple Feature metadata used for id-based filtering, with arguments will `where` parameter when selecting features to retain, or be merged) with `exclude-ids` when selecting features to discard. [optional]" name="additional_input" optional="True" type="data" />
81 </repeat>
82 <param label="--p-where: TEXT SQLite WHERE clause specifying feature metadata criteria that must be met to be included in the filtered feature table. If not provided, all features in `metadata` that are also in the sequences will be retained. [optional]" name="pwhere" optional="False" type="text" />
83 <param label="--p-exclude-ids: --p-exclude-ids: / --p-no-exclude-ids If true, the features selected by the `metadata` (with or without the `where` parameter) or `table` parameter will be excluded from the filtered sequences instead of being retained. [default: False]" name="pexcludeids" selected="False" type="boolean" />
84 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
85
86 </inputs>
87
88 <outputs>
89 <data format="qza" label="${tool.name} on ${on_string}: filtereddata.qza" name="ofiltereddata" />
90
91 </outputs>
92
93 <help><![CDATA[
94 Filter features from sequences
95 ###############################################################
96
97 Filter features from sequences based on a feature table or metadata. See
98 the filtering tutorial on https://docs.qiime2.org for additional details.
99 This method can filter based on ids in a table or a metadata file, but not
100 both (i.e., the table and metadata options are mutually exclusive).
101
102 Parameters
103 ----------
104 data : FeatureData[Sequence¹ | AlignedSequence²]
105 The sequences from which features should be filtered.
106 table : FeatureTable[Frequency], optional
107 Table containing feature ids used for id-based filtering.
108 metadata : Metadata, optional
109 Feature metadata used for id-based filtering, with `where` parameter
110 when selecting features to retain, or with `exclude_ids` when selecting
111 features to discard.
112 where : Str, optional
113 SQLite WHERE clause specifying feature metadata criteria that must be
114 met to be included in the filtered feature table. If not provided, all
115 features in `metadata` that are also in the sequences will be retained.
116 exclude_ids : Bool, optional
117 If true, the features selected by the `metadata` (with or without the
118 `where` parameter) or `table` parameter will be excluded from the
119 filtered sequences instead of being retained.
120
121 Returns
122 -------
123 filtered_data : FeatureData[Sequence¹ | AlignedSequence²]
124 The resulting filtered sequences.
125 ]]></help>
126 <macros>
127 <import>qiime_citation.xml</import>
128 </macros>
129 <expand macro="qiime_citation"/>
130 </tool>