Mercurial > repos > florianbegusch > qiime2_suite
comparison qiime2/qiime_demux_filter-samples.xml @ 6:de4c22a52df4 draft
Fixes
author | florianbegusch |
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date | Tue, 13 Aug 2019 07:46:48 -0400 |
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5:a025a4a89e07 | 6:de4c22a52df4 |
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1 <?xml version="1.0" ?> | |
2 <tool id="qiime_demux_filter-samples" name="qiime demux filter-samples" version="2019.7"> | |
3 <description> - Filter samples out of demultiplexed data.</description> | |
4 <requirements> | |
5 <requirement type="package" version="2019.7">qiime2</requirement> | |
6 </requirements> | |
7 <command><![CDATA[ | |
8 qiime demux filter-samples | |
9 | |
10 --i-demux=$idemux | |
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($input_files_mmetadatafile) | |
22 #end if | |
23 | |
24 | |
25 | |
26 #if '__sq__' in str($pwhere): | |
27 #set $pwhere_temp = $pwhere.replace('__sq__', "'") | |
28 #set $pwhere = $pwhere_temp | |
29 #end if | |
30 | |
31 | |
32 #if str($pwhere): | |
33 --p-where="$pwhere" | |
34 #end if | |
35 | |
36 | |
37 #if $pexcludeids: | |
38 --p-exclude-ids | |
39 #end if | |
40 | |
41 #if str($citations) != 'None': | |
42 --citations=$citations | |
43 #end if | |
44 | |
45 | |
46 --o-filtered-demux=ofiltereddemux | |
47 | |
48 ; | |
49 cp ofiltereddemux.qza $ofiltereddemux | |
50 ]]></command> | |
51 <inputs> | |
52 | |
53 <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file"> | |
54 <param label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. Sample metadata file containing individual_id_column. [required]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" /> | |
55 </repeat> | |
56 | |
57 <param format="qza,no_unzip.zip" label="--i-demux: ARTIFACT SampleData[SequencesWithQuality¹ | PairedEndSequencesWithQuality² | JoinedSequencesWithQuality³] The demultiplexed data from which samples should be filtered. [required]" name="idemux" optional="False" type="data"/> | |
58 <param label="--p-where: TEXT Optional SQLite WHERE clause specifying sample metadata criteria that must be met to be included in the filtered data. If not provided, all samples in `metadata` that are also in the demultiplexed data will be retained. [optional]" name="pwhere" optional="True" type="text"/> | |
59 <param label="--p-exclude-ids: --p-no-exclude-ids Defaults to False. If True, the samples selected by the `metadata` and optional `where` parameter will be excluded from the filtered data. [default: False]" name="pexcludeids" selected="False" type="boolean"/> | |
60 </inputs> | |
61 <outputs> | |
62 <data format="qza" label="${tool.name} on ${on_string}: filtereddemux.qza" name="ofiltereddemux"/> | |
63 </outputs> | |
64 <help><![CDATA[ | |
65 | |
66 ]]></help> | |
67 <macros> | |
68 <import>qiime_citation.xml</import> | |
69 </macros> | |
70 <expand macro="qiime_citation"/> | |
71 </tool> |