Mercurial > repos > florianbegusch > qiime2_suite
comparison qiime2/qiime_feature-table_filter-seqs.xml @ 29:3ba9833030c1 draft
Uploaded
author | florianbegusch |
---|---|
date | Fri, 04 Sep 2020 13:12:49 +0000 |
parents | |
children |
comparison
equal
deleted
inserted
replaced
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> |