Mercurial > repos > florianbegusch > qiime2_suite
comparison qiime2/qiime_feature-table_filter-samples.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 | a025a4a89e07 |
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1 <?xml version="1.0" ?> | |
2 <tool id="qiime_feature-table_filter-samples" name="qiime feature-table filter-samples" version="2019.4"> | |
3 <description> - Filter samples from table</description> | |
4 <requirements> | |
5 <requirement type="package" version="2019.4">qiime2</requirement> | |
6 </requirements> | |
7 <command><![CDATA[ | |
8 qiime feature-table filter-samples | |
9 | |
10 --i-table=$itable | |
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 $pminfrequency: | |
26 --p-min-frequency=$pminfrequency | |
27 #end if | |
28 | |
29 #if str($pmaxfrequency): | |
30 --p-max-frequency="$pmaxfrequency" | |
31 #end if | |
32 | |
33 #if $pminfeatures: | |
34 --p-min-features=$pminfeatures | |
35 #end if | |
36 | |
37 #if str($pmaxfeatures): | |
38 --p-max-features="$pmaxfeatures" | |
39 #end if | |
40 | |
41 #if '__sq__' in str($pwhere): | |
42 #set $pwhere_temp = $pwhere.replace('__sq__', "'") | |
43 #set $pwhere = $pwhere_temp | |
44 #end if | |
45 | |
46 #if str($pwhere): | |
47 --p-where="$pwhere" | |
48 #end if | |
49 | |
50 | |
51 #if $pexcludeids: | |
52 --p-exclude-ids | |
53 #end if | |
54 | |
55 --o-filtered-table=ofilteredtable | |
56 ; | |
57 cp ofilteredtable.qza $ofilteredtable | |
58 ]]></command> | |
59 <inputs> | |
60 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency¹ | RelativeFrequency² | PresenceAbsence³ | Composition⁴] The feature table from which samples should be filtered. [required]" name="itable" optional="False" type="data"/> | |
61 <param label="--p-min-frequency: INTEGER The minimum total frequency that a sample must have to be retained. [default: 0]" name="pminfrequency" optional="True" type="integer" value="0"/> | |
62 <param label="--p-max-frequency: INTEGER The maximum total frequency that a sample can have to be retained. If no value is provided this will default to infinity (i.e., no maximum frequency filter will be applied). [optional]" name="pmaxfrequency" optional="True" type="integer"/> | |
63 <param label="--p-min-features: INTEGER The minimum number of features that a sample must have to be retained. [default: 0]" name="pminfeatures" optional="True" type="integer" value="0"/> | |
64 <param label="--p-max-features: INTEGER The maximum number of features that a sample can have to be retained. If no value is provided this will default to infinity (i.e., no maximum feature filter will be applied). [optional]" name="pmaxfeatures" optional="True" type="integer"/> | |
65 <param label="--p-where: TEXT SQLite WHERE clause specifying sample metadata criteria that must be met to be included in the filtered feature table. If not provided, all samples in `metadata` that are also in the feature table will be retained. [optional]" name="pwhere" optional="True" type="text"/> | |
66 <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 table instead of being retained. [default: False]" name="pexcludeids" selected="False" type="boolean"/> | |
67 | |
68 <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file"> | |
69 <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" /> | |
70 </repeat> | |
71 </inputs> | |
72 <outputs> | |
73 <data format="qza" label="${tool.name} on ${on_string}: filteredtable.qza" name="ofilteredtable"/> | |
74 </outputs> | |
75 <help><![CDATA[ | |
76 Filter samples from table | |
77 ######################### | |
78 | |
79 Filter samples from table based on frequency and/or metadata. Any features | |
80 with a frequency of zero after sample filtering will also be removed. See | |
81 the filtering tutorial on https://docs.qiime2.org for additional details. | |
82 | |
83 Parameters | |
84 ---------- | |
85 table : FeatureTable[Frequency¹ | RelativeFrequency² | PresenceAbsence³ | Composition⁴] | |
86 The feature table from which samples should be filtered. | |
87 min_frequency : Int, optional | |
88 The minimum total frequency that a sample must have to be retained. | |
89 max_frequency : Int, optional | |
90 The maximum total frequency that a sample can have to be retained. If | |
91 no value is provided this will default to infinity (i.e., no maximum | |
92 frequency filter will be applied). | |
93 min_features : Int, optional | |
94 The minimum number of features that a sample must have to be retained. | |
95 max_features : Int, optional | |
96 The maximum number of features that a sample can have to be retained. | |
97 If no value is provided this will default to infinity (i.e., no maximum | |
98 feature filter will be applied). | |
99 metadata : Metadata, optional | |
100 Sample metadata used with `where` parameter when selecting samples to | |
101 retain, or with `exclude_ids` when selecting samples to discard. | |
102 where : Str, optional | |
103 SQLite WHERE clause specifying sample metadata criteria that must be | |
104 met to be included in the filtered feature table. If not provided, all | |
105 samples in `metadata` that are also in the feature table will be | |
106 retained. | |
107 exclude_ids : Bool, optional | |
108 If true, the samples selected by `metadata` or `where` parameters will | |
109 be excluded from the filtered table instead of being retained. | |
110 | |
111 Returns | |
112 ------- | |
113 filtered_table : FeatureTable[Frequency¹ | RelativeFrequency² | PresenceAbsence³ | Composition⁴] | |
114 The resulting feature table filtered by sample. | |
115 ]]></help> | |
116 <macros> | |
117 <import>qiime_citation.xml</import> | |
118 </macros> | |
119 <expand macro="qiime_citation"/> | |
120 </tool> |