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comparison qiime2/qiime_feature-table_filter-samples.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-samples" name="qiime feature-table filter-samples"
3 version="2020.8">
4 <description>Filter samples from table</description>
5 <requirements>
6 <requirement type="package" version="2020.8">qiime2</requirement>
7 </requirements>
8 <command><![CDATA[
9 qiime feature-table filter-samples
10
11 --i-table=$itable
12
13 --p-min-frequency=$pminfrequency
14
15 #if str($pmaxfrequency):
16 --p-max-frequency=$pmaxfrequency
17 #end if
18 --p-min-features=$pminfeatures
19
20 #if str($pmaxfeatures):
21 --p-max-features=$pmaxfeatures
22 #end if# if $input_files_mmetadatafile:
23 # def list_dict_to_string(list_dict):
24 # set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
25 # for d in list_dict[1:]:
26 # set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
27 # end for
28 # return $file_list
29 # end def
30 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
31 # end if
32
33 #if '__ob__' in str($pwhere):
34 #set $pwhere_temp = $pwhere.replace('__ob__', '[')
35 #set $pwhere = $pwhere_temp
36 #end if
37 #if '__cb__' in str($pwhere):
38 #set $pwhere_temp = $pwhere.replace('__cb__', ']')
39 #set $pwhere = $pwhere_temp
40 #end if
41 #if 'X' in str($pwhere):
42 #set $pwhere_temp = $pwhere.replace('X', '\\')
43 #set $pwhere = $pwhere_temp
44 #end if
45 #if '__sq__' in str($pwhere):
46 #set $pwhere_temp = $pwhere.replace('__sq__', "'")
47 #set $pwhere = $pwhere_temp
48 #end if
49 #if '__db__' in str($pwhere):
50 #set $pwhere_temp = $pwhere.replace('__db__', '"')
51 #set $pwhere = $pwhere_temp
52 #end if
53
54 #if str($pwhere):
55 --p-where=$pwhere
56 #end if
57
58 #if $pexcludeids:
59 --p-exclude-ids
60 #end if
61
62 --o-filtered-table=ofilteredtable
63
64 #if str($examples) != 'None':
65 --examples=$examples
66 #end if
67
68 ;
69 cp ofilteredtable.qza $ofilteredtable
70
71 ]]></command>
72 <inputs>
73 <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" />
74 <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" />
75 <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="False" type="text" />
76 <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" />
77 <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="False" type="text" />
78 <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file">
79 <param format="tabular,qza,no_unzip.zip" label="--m-metadata-file: METADATA... (multiple Sample metadata used with `where` parameter when arguments will selecting samples to retain, or with `exclude-ids` when be merged) selecting samples to discard. [optional]" name="additional_input" optional="True" type="data" />
80 </repeat>
81 <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="False" type="text" />
82 <param label="--p-exclude-ids: --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" />
83 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
84
85 </inputs>
86
87 <outputs>
88 <data format="qza" label="${tool.name} on ${on_string}: filteredtable.qza" name="ofilteredtable" />
89
90 </outputs>
91
92 <help><![CDATA[
93 Filter samples from table
94 ###############################################################
95
96 Filter samples from table based on frequency and/or metadata. Any features
97 with a frequency of zero after sample filtering will also be removed. See
98 the filtering tutorial on https://docs.qiime2.org for additional details.
99
100 Parameters
101 ----------
102 table : FeatureTable[Frequency¹ | RelativeFrequency² | PresenceAbsence³ | Composition⁴]
103 The feature table from which samples should be filtered.
104 min_frequency : Int, optional
105 The minimum total frequency that a sample must have to be retained.
106 max_frequency : Int, optional
107 The maximum total frequency that a sample can have to be retained. If
108 no value is provided this will default to infinity (i.e., no maximum
109 frequency filter will be applied).
110 min_features : Int, optional
111 The minimum number of features that a sample must have to be retained.
112 max_features : Int, optional
113 The maximum number of features that a sample can have to be retained.
114 If no value is provided this will default to infinity (i.e., no maximum
115 feature filter will be applied).
116 metadata : Metadata, optional
117 Sample metadata used with `where` parameter when selecting samples to
118 retain, or with `exclude_ids` when selecting samples to discard.
119 where : Str, optional
120 SQLite WHERE clause specifying sample metadata criteria that must be
121 met to be included in the filtered feature table. If not provided, all
122 samples in `metadata` that are also in the feature table will be
123 retained.
124 exclude_ids : Bool, optional
125 If true, the samples selected by `metadata` or `where` parameters will
126 be excluded from the filtered table instead of being retained.
127
128 Returns
129 -------
130 filtered_table : FeatureTable[Frequency¹ | RelativeFrequency² | PresenceAbsence³ | Composition⁴]
131 The resulting feature table filtered by sample.
132 ]]></help>
133 <macros>
134 <import>qiime_citation.xml</import>
135 </macros>
136 <expand macro="qiime_citation"/>
137 </tool>