Mercurial > repos > florianbegusch > qiime2_suite
diff qiime2/qiime_demux_filter-samples.xml @ 14:a0a8d77a991c draft
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author | florianbegusch |
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date | Thu, 03 Sep 2020 09:51:29 +0000 |
parents | f190567fe3f6 |
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--- a/qiime2/qiime_demux_filter-samples.xml Thu Sep 03 09:46:00 2020 +0000 +++ b/qiime2/qiime_demux_filter-samples.xml Thu Sep 03 09:51:29 2020 +0000 @@ -1,65 +1,83 @@ <?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 - +<tool id="qiime_demux_filter-samples" name="qiime demux filter-samples" + version="2020.8"> + <description>Filter samples out of demultiplexed data.</description> + <requirements> + <requirement type="package" version="2020.8">qiime2</requirement> + </requirements> + <command><![CDATA[ +qiime demux filter-samples -#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($input_files_mmetadatafile) +--i-demux=$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($input_files_mmetadatafile) +# end if + +#if '__ob__' in str($pwhere): + #set $pwhere_temp = $pwhere.replace('__ob__', '[') + #set $pwhere = $pwhere_temp #end if - - - +#if '__cb__' in str($pwhere): + #set $pwhere_temp = $pwhere.replace('__cb__', ']') + #set $pwhere = $pwhere_temp +#end if +#if 'X' in str($pwhere): + #set $pwhere_temp = $pwhere.replace('X', '\\') + #set $pwhere = $pwhere_temp +#end if #if '__sq__' in str($pwhere): #set $pwhere_temp = $pwhere.replace('__sq__', "'") #set $pwhere = $pwhere_temp #end if - +#if '__db__' in str($pwhere): + #set $pwhere_temp = $pwhere.replace('__db__', '"') + #set $pwhere = $pwhere_temp +#end if #if str($pwhere): - --p-where="$pwhere" + --p-where=$pwhere #end if - #if $pexcludeids: --p-exclude-ids #end if +--o-filtered-demux=ofiltereddemux ---o-filtered-demux=ofiltereddemux +#if str($examples) != 'None': +--examples=$examples +#end if ; 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 ${on_string}: filtereddemux.qza" name="ofiltereddemux"/> - </outputs> - <help><![CDATA[ + ]]></command> + <inputs> + <param format="qza,no_unzip.zip" label="--i-demux: ARTIFACT SampleData[SequencesWithQuality¹ | PairedEndSequencesWithQuality² | JoinedSequencesWithQuality³] The demultiplexed data from which samples should be filtered. [required]" name="idemux" optional="False" type="data" /> + <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file"> + <param format="tabular,qza,no_unzip.zip" label="--m-metadata-file: METADATA... (multiple Sample metadata indicating which sample ids to filter. arguments will The optional `where` parameter may be used to filter be merged) ids based on specified conditions in the metadata. The optional `exclude-ids` parameter may be used to exclude the ids specified in the metadata from the filter. [required]" name="additional_input" optional="False" type="data" /> + </repeat> + <param label="--p-where: TEXT Optional SQLite WHERE clause specifying sample metadata criteria that must be met to be included in the filtered data. If not provided, all samples in `metadata` that are also in the demultiplexed data will be retained. [optional]" name="pwhere" optional="False" type="text" /> + <param label="--p-exclude-ids: --p-exclude-ids: / --p-no-exclude-ids Defaults to False. If True, the samples selected by the `metadata` and optional `where` parameter will be excluded from the filtered data. [default: False]" name="pexcludeids" selected="False" type="boolean" /> + <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" /> + + </inputs> + + <outputs> + <data format="qza" label="${tool.name} on ${on_string}: filtereddemux.qza" name="ofiltereddemux" /> + + </outputs> + + <help><![CDATA[ Filter samples out of demultiplexed data. -######################################### +############################################################### Filter samples indicated in given metadata out of demultiplexed data. Specific samples can be further selected with the WHERE clause, and the @@ -87,9 +105,9 @@ ------- filtered_demux : SampleData[SequencesWithQuality¹ | PairedEndSequencesWithQuality² | JoinedSequencesWithQuality³] Filtered demultiplexed data. - ]]></help> -<macros> + ]]></help> + <macros> <import>qiime_citation.xml</import> -</macros> -<expand macro="qiime_citation"/> -</tool> + </macros> + <expand macro="qiime_citation"/> +</tool> \ No newline at end of file