Mercurial > repos > florianbegusch > qiime2_suite
comparison qiime2-2020.8/qiime_demux_filter-samples.xml @ 20:d93d8888f0b0 draft
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author | florianbegusch |
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date | Fri, 04 Sep 2020 12:44:24 +0000 |
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19:6c48f8d82424 | 20:d93d8888f0b0 |
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1 <?xml version="1.0" ?> | |
2 <tool id="qiime_demux_filter-samples" name="qiime demux filter-samples" | |
3 version="2020.8"> | |
4 <description>Filter samples out of demultiplexed data.</description> | |
5 <requirements> | |
6 <requirement type="package" version="2020.8">qiime2</requirement> | |
7 </requirements> | |
8 <command><![CDATA[ | |
9 qiime demux filter-samples | |
10 | |
11 --i-demux=$idemux | |
12 # if $input_files_mmetadatafile: | |
13 # def list_dict_to_string(list_dict): | |
14 # set $file_list = list_dict[0]['additional_input'].__getattr__('file_name') | |
15 # for d in list_dict[1:]: | |
16 # set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name') | |
17 # end for | |
18 # return $file_list | |
19 # end def | |
20 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile) | |
21 # end if | |
22 | |
23 #if '__ob__' in str($pwhere): | |
24 #set $pwhere_temp = $pwhere.replace('__ob__', '[') | |
25 #set $pwhere = $pwhere_temp | |
26 #end if | |
27 #if '__cb__' in str($pwhere): | |
28 #set $pwhere_temp = $pwhere.replace('__cb__', ']') | |
29 #set $pwhere = $pwhere_temp | |
30 #end if | |
31 #if 'X' in str($pwhere): | |
32 #set $pwhere_temp = $pwhere.replace('X', '\\') | |
33 #set $pwhere = $pwhere_temp | |
34 #end if | |
35 #if '__sq__' in str($pwhere): | |
36 #set $pwhere_temp = $pwhere.replace('__sq__', "'") | |
37 #set $pwhere = $pwhere_temp | |
38 #end if | |
39 #if '__db__' in str($pwhere): | |
40 #set $pwhere_temp = $pwhere.replace('__db__', '"') | |
41 #set $pwhere = $pwhere_temp | |
42 #end if | |
43 | |
44 #if str($pwhere): | |
45 --p-where=$pwhere | |
46 #end if | |
47 | |
48 #if $pexcludeids: | |
49 --p-exclude-ids | |
50 #end if | |
51 | |
52 --o-filtered-demux=ofiltereddemux | |
53 | |
54 #if str($examples) != 'None': | |
55 --examples=$examples | |
56 #end if | |
57 | |
58 ; | |
59 cp ofiltereddemux.qza $ofiltereddemux | |
60 | |
61 ]]></command> | |
62 <inputs> | |
63 <param format="qza,no_unzip.zip" label="--i-demux: ARTIFACT SampleData[SequencesWithQuality¹ | PairedEndSequencesWithQuality² | JoinedSequencesWithQuality³] The demultiplexed data from which samples should be filtered. [required]" name="idemux" optional="False" type="data" /> | |
64 <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file"> | |
65 <param format="tabular,qza,no_unzip.zip" label="--m-metadata-file: METADATA... (multiple Sample metadata indicating which sample ids to filter. arguments will The optional `where` parameter may be used to filter be merged) ids based on specified conditions in the metadata. The optional `exclude-ids` parameter may be used to exclude the ids specified in the metadata from the filter. [required]" name="additional_input" optional="False" type="data" /> | |
66 </repeat> | |
67 <param label="--p-where: TEXT Optional SQLite WHERE clause specifying sample metadata criteria that must be met to be included in the filtered data. If not provided, all samples in `metadata` that are also in the demultiplexed data will be retained. [optional]" name="pwhere" optional="False" type="text" /> | |
68 <param label="--p-exclude-ids: --p-exclude-ids: / --p-no-exclude-ids Defaults to False. If True, the samples selected by the `metadata` and optional `where` parameter will be excluded from the filtered data. [default: False]" name="pexcludeids" selected="False" type="boolean" /> | |
69 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" /> | |
70 | |
71 </inputs> | |
72 | |
73 <outputs> | |
74 <data format="qza" label="${tool.name} on ${on_string}: filtereddemux.qza" name="ofiltereddemux" /> | |
75 | |
76 </outputs> | |
77 | |
78 <help><![CDATA[ | |
79 Filter samples out of demultiplexed data. | |
80 ############################################################### | |
81 | |
82 Filter samples indicated in given metadata out of demultiplexed data. | |
83 Specific samples can be further selected with the WHERE clause, and the | |
84 `exclude_ids` parameter allows for filtering of all samples not specified. | |
85 | |
86 Parameters | |
87 ---------- | |
88 demux : SampleData[SequencesWithQuality¹ | PairedEndSequencesWithQuality² | JoinedSequencesWithQuality³] | |
89 The demultiplexed data from which samples should be filtered. | |
90 metadata : Metadata | |
91 Sample metadata indicating which sample ids to filter. The optional | |
92 `where` parameter may be used to filter ids based on specified | |
93 conditions in the metadata. The optional `exclude_ids` parameter may be | |
94 used to exclude the ids specified in the metadata from the filter. | |
95 where : Str, optional | |
96 Optional SQLite WHERE clause specifying sample metadata criteria that | |
97 must be met to be included in the filtered data. If not provided, all | |
98 samples in `metadata` that are also in the demultiplexed data will be | |
99 retained. | |
100 exclude_ids : Bool, optional | |
101 Defaults to False. If True, the samples selected by the `metadata` and | |
102 optional `where` parameter will be excluded from the filtered data. | |
103 | |
104 Returns | |
105 ------- | |
106 filtered_demux : SampleData[SequencesWithQuality¹ | PairedEndSequencesWithQuality² | JoinedSequencesWithQuality³] | |
107 Filtered demultiplexed data. | |
108 ]]></help> | |
109 <macros> | |
110 <import>qiime_citation.xml</import> | |
111 </macros> | |
112 <expand macro="qiime_citation"/> | |
113 </tool> |