Mercurial > repos > florianbegusch > qiime2_suite
diff 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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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_demux_filter-samples.xml Tue Aug 13 07:46:48 2019 -0400 @@ -0,0 +1,71 @@ +<?xml version="1.0" ?> +<tool id="qiime_demux_filter-samples" name="qiime demux filter-samples" version="2019.7"> + <description> - Filter samples out of demultiplexed data.</description> + <requirements> + <requirement type="package" version="2019.7">qiime2</requirement> + </requirements> + <command><![CDATA[ +qiime demux filter-samples + +--i-demux=$idemux + + +#if $input_files_mmetadatafile: +#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 + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name') + #end for + #return $file_list +#end def + --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile) +#end if + + + +#if '__sq__' in str($pwhere): + #set $pwhere_temp = $pwhere.replace('__sq__', "'") + #set $pwhere = $pwhere_temp +#end if + + +#if str($pwhere): + --p-where="$pwhere" +#end if + + +#if $pexcludeids: + --p-exclude-ids +#end if + +#if str($citations) != 'None': + --citations=$citations +#end if + + +--o-filtered-demux=ofiltereddemux + +; +cp ofiltereddemux.qza $ofiltereddemux + ]]></command> + <inputs> + + <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file"> + <param label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. Sample metadata file containing individual_id_column. [required]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" /> + </repeat> + + <param format="qza,no_unzip.zip" label="--i-demux: ARTIFACT SampleData[SequencesWithQuality¹ | PairedEndSequencesWithQuality² | JoinedSequencesWithQuality³] The demultiplexed data from which samples should be filtered. [required]" name="idemux" optional="False" type="data"/> + <param label="--p-where: TEXT Optional SQLite WHERE clause specifying sample metadata criteria that must be met to be included in the filtered data. If not provided, all samples in `metadata` that are also in the demultiplexed data will be retained. [optional]" name="pwhere" optional="True" type="text"/> + <param label="--p-exclude-ids: --p-no-exclude-ids Defaults to False. If True, the samples selected by the `metadata` and optional `where` parameter will be excluded from the filtered data. [default: False]" name="pexcludeids" selected="False" type="boolean"/> + </inputs> + <outputs> + <data format="qza" label="${tool.name} on ${on_string}: filtereddemux.qza" name="ofiltereddemux"/> + </outputs> + <help><![CDATA[ + + ]]></help> +<macros> + <import>qiime_citation.xml</import> +</macros> +<expand macro="qiime_citation"/> +</tool>