Mercurial > repos > florianbegusch > qiime2_suite
comparison qiime2/qiime_diversity_filter-distance-matrix.xml @ 0:370e0b6e9826 draft
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author | florianbegusch |
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date | Wed, 17 Jul 2019 03:05:17 -0400 |
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children | 914fa4daf16a |
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1 <?xml version="1.0" ?> | |
2 <tool id="qiime_diversity_filter-distance-matrix" name="qiime diversity filter-distance-matrix" version="2019.4"> | |
3 <description> - Filter samples from a distance matrix.</description> | |
4 <requirements> | |
5 <requirement type="package" version="2019.4">qiime2</requirement> | |
6 </requirements> | |
7 <command><![CDATA[ | |
8 qiime diversity filter-distance-matrix | |
9 | |
10 --i-distance-matrix=$idistancematrix | |
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($input_files_mmetadatafile) | |
22 #end if | |
23 | |
24 | |
25 #if '__sq__' in str($pwhere): | |
26 #set $pwhere_temp = $pwhere.replace('__sq__', "'") | |
27 #set $pwhere = $pwhere_temp | |
28 #end if | |
29 | |
30 #if str($pwhere): | |
31 --p-where="$pwhere" | |
32 #end if | |
33 | |
34 | |
35 #if $pexcludeids: | |
36 --p-exclude-ids | |
37 #end if | |
38 | |
39 --o-filtered-distance-matrix=ofiltereddistancematrix | |
40 ; | |
41 cp ofiltereddistancematrix.qza $ofiltereddistancematrix | |
42 ]]></command> | |
43 <inputs> | |
44 <param format="qza,no_unzip.zip" label="--i-distance-matrix: ARTIFACT DistanceMatrix Distance matrix to filter by sample. [required]" name="idistancematrix" optional="False" type="data"/> | |
45 <param label="--p-where: TEXT SQLite WHERE clause specifying sample metadata criteria that must be met to be included in the filtered distance matrix. If not provided, all samples in `metadata` that are also in the input distance matrix will be retained. [optional]" name="pwhere" optional="True" type="text"/> | |
46 <param label="--p-exclude-ids: --p-no-exclude-ids If `True`, the samples selected by `metadata` or `where` parameters will be excluded from the filtered distance matrix instead of being retained. [default: False]" name="pexcludeids" selected="False" type="boolean"/> | |
47 | |
48 <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file"> | |
49 <param label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [optional]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" /> | |
50 </repeat> | |
51 | |
52 </inputs> | |
53 <outputs> | |
54 <data format="qza" label="${tool.name} on ${on_string}: filtereddistancematrix.qza" name="ofiltereddistancematrix"/> | |
55 </outputs> | |
56 <help><![CDATA[ | |
57 Filter samples from a distance matrix. | |
58 ###################################### | |
59 | |
60 Filter samples from a distance matrix, retaining only the samples matching | |
61 search criteria specified by `metadata` and `where` parameters (or | |
62 retaining only the samples not matching that criteria, if `exclude_ids` is | |
63 True). See the filtering tutorial on https://docs.qiime2.org for additional | |
64 details. | |
65 | |
66 Parameters | |
67 ---------- | |
68 distance_matrix : DistanceMatrix | |
69 Distance matrix to filter by sample. | |
70 metadata : Metadata | |
71 Sample metadata used with `where` parameter when selecting samples to | |
72 retain, or with `exclude_ids` when selecting samples to discard. | |
73 where : Str, optional | |
74 SQLite WHERE clause specifying sample metadata criteria that must be | |
75 met to be included in the filtered distance matrix. If not provided, | |
76 all samples in `metadata` that are also in the input distance matrix | |
77 will be retained. | |
78 exclude_ids : Bool, optional | |
79 If `True`, the samples selected by `metadata` or `where` parameters | |
80 will be excluded from the filtered distance matrix instead of being | |
81 retained. | |
82 | |
83 Returns | |
84 ------- | |
85 filtered_distance_matrix : DistanceMatrix | |
86 Distance matrix filtered to include samples matching search criteria | |
87 ]]></help> | |
88 <macros> | |
89 <import>qiime_citation.xml</import> | |
90 </macros> | |
91 <expand macro="qiime_citation"/> | |
92 </tool> |