Mercurial > repos > florianbegusch > qiime2_wrappers

comparison qiime2/qiime_demux_emp-single.xml @ 4:71f124e02000 draft default tip

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Fixes
author florianbegusch
date Tue, 13 Aug 2019 07:40:25 -0400
parents 149432539226
children
comparison
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3:eda5df31da55 4:71f124e02000
9 9
10 --i-seqs=$iseqs 10 --i-seqs=$iseqs
11 --m-barcodes-column="$mbarcodescolumn" 11 --m-barcodes-column="$mbarcodescolumn"
12 12
13 13
14 #if $input_files_mbarcodesfile:
14 #def list_dict_to_string(list_dict): 15 #def list_dict_to_string(list_dict):
15 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name') 16 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
16 #for d in list_dict[1:]: 17 #for d in list_dict[1:]:
17 #set $file_list = $file_list + ',' + d['additional_input'].__getattr__('file_name') 18 #set $file_list = $file_list + ',' + d['additional_input'].__getattr__('file_name')
18 #end for 19 #end for
19 #return $file_list 20 #return $file_list
20 #end def 21 #end def
21
22 --m-barcodes-file=$list_dict_to_string($input_files_mbarcodesfile) 22 --m-barcodes-file=$list_dict_to_string($input_files_mbarcodesfile)
23 #end if
23 24
24 25
25 #if $pnogolayerrorcorrection: 26 #if $pnogolayerrorcorrection:
26 --p-no-golay-error-correction 27 --p-no-golay-error-correction
27 #end if 28 #end if
39 ; 40 ;
40 cp opersamplesequences.qza $opersamplesequences; 41 cp opersamplesequences.qza $opersamplesequences;
41 cp oerrorcorrectiondetails.qza $oerrorcorrectiondetails 42 cp oerrorcorrectiondetails.qza $oerrorcorrectiondetails
42 ]]></command> 43 ]]></command>
43 <inputs> 44 <inputs>
44 <repeat name="input_files_mbarcodesfile" optional="False" title="--m-barcodes-file"> 45 <repeat name="input_files_mbarcodesfile" optional="True" title="--m-barcodes-file [optional]">
45 <param label="--m-barcodes-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [required]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip"/> 46 <param label="--m-barcodes-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"/>
46 </repeat> 47 </repeat>
47 48
48 <param format="qza,no_unzip.zip" label="--i-seqs: ARTIFACT RawSequences | EMPSingleEndSequences | EMPPairedEndSequences The single-end sequences to be demultiplexed. [required]" name="iseqs" optional="False" type="data"/> 49 <param format="qza,no_unzip.zip" label="--i-seqs: ARTIFACT RawSequences | EMPSingleEndSequences | EMPPairedEndSequences The single-end sequences to be demultiplexed. [required]" name="iseqs" optional="False" type="data"/>
49 <param label="--m-barcodes-column: COLUMN MetadataColumn[Categorical] The sample metadata column containing the per-sample barcodes. [required]" name="mbarcodescolumn" optional="False" type="text"/> 50 <param label="--m-barcodes-column: COLUMN MetadataColumn[Categorical] The sample metadata column containing the per-sample barcodes. [required]" name="mbarcodescolumn" optional="False" type="text"/>
50 <param label="--p-no-golay-error-correction: Do not perform 12nt Golay error correction on the barcode reads. [default: False]" name="pnogolayerrorcorrection" selected="False" type="boolean"/> 51 <param label="--p-no-golay-error-correction: Do not perform 12nt Golay error correction on the barcode reads. [default: False]" name="pnogolayerrorcorrection" selected="False" type="boolean"/>