Mercurial > repos > florianbegusch > qiime2_suite
diff qiime2/qiime_cutadapt_demux-single.xml @ 4:914fa4daf16a draft
Fixes
author | florianbegusch |
---|---|
date | Wed, 31 Jul 2019 03:06:00 -0400 |
parents | 51025741f326 |
children | f190567fe3f6 |
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--- a/qiime2/qiime_cutadapt_demux-single.xml Sun Jul 21 02:21:34 2019 -0400 +++ b/qiime2/qiime_cutadapt_demux-single.xml Wed Jul 31 03:06:00 2019 -0400 @@ -8,22 +8,37 @@ qiime cutadapt demux-single --i-seqs=$iseqs + + + +#if '__sq__' in str($mbarcodescolumn): + #set $mbarcodescolumn_temp = $mbarcodescolumn.replace('__sq__', "'") + #set $mbarcodescolumn = $mbarcodescolumn_temp +#end if + --m-barcodes-column="$mbarcodescolumn" + + --o-per-sample-sequences=opersamplesequences --o-untrimmed-sequences=ountrimmedsequences + + + + #if $input_files_mbarcodesfile: #def list_dict_to_string(list_dict): - #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name') - #for d in list_dict[1:]: - #set $file_list = $file_list + ',' + d['additional_input'].__getattr__('file_name') - #end for - #return $file_list +#set $file_list = list_dict[0]['additional_input'].__getattr__('file_name') +#for d in list_dict[1:]: + #set $file_list = $file_list + ',' + d['additional_input'].__getattr__('file_name') +#end for +#return $file_list #end def ---m-barcodes-file=$list_dict_to_string("$input_files_mbarcodesfile") +--m-barcodes-file=$list_dict_to_string($input_files_mbarcodesfile) #end if + #if $perrorrate: --p-error-rate=$perrorrate #end if @@ -35,7 +50,7 @@ ]]></command> <inputs> <param format="qza,no_unzip.zip" label="--i-seqs: ARTIFACT MultiplexedSingleEndBarcodeInSequence The single-end sequences to be demultiplexed. [required]" name="iseqs" optional="False" type="data"/> - <repeat name="$input_files_mbarcodesfile" optional="False" title="--m-barcodes-file"> + <repeat name="input_files_mbarcodesfile" optional="False" title="--m-barcodes-file"> <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" /> </repeat> <param label="--m-barcodes-column: COLUMN MetadataColumn[Categorical] The sample metadata column listing the per-sample barcodes. [required]" name="mbarcodescolumn" optional="False" type="text"/>