Mercurial > repos > florianbegusch > qiime2_suite
diff qiime2/qiime_feature-table_merge.xml @ 29:3ba9833030c1 draft
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author | florianbegusch |
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date | Fri, 04 Sep 2020 13:12:49 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_feature-table_merge.xml Fri Sep 04 13:12:49 2020 +0000 @@ -0,0 +1,76 @@ +<?xml version="1.0" ?> +<tool id="qiime_feature-table_merge" name="qiime feature-table merge" + version="2020.8"> + <description>Combine multiple tables</description> + <requirements> + <requirement type="package" version="2020.8">qiime2</requirement> + </requirements> + <command><![CDATA[ +qiime feature-table merge +# if $input_files_itables: + # 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 + ' --i-tables=' + d['additional_input'].__getattr__('file_name') + # end for + # return $file_list + # end def +--i-tables=$list_dict_to_string($input_files_itables) +# end if + +#if str($poverlapmethod) != 'None': +--p-overlap-method=$poverlapmethod +#end if + +--o-merged-table=omergedtable + +#if str($examples) != 'None': +--examples=$examples +#end if + +; +cp omergedtable.qza $omergedtable + + ]]></command> + <inputs> + <repeat name="input_files_itables" optional="False" title="--i-tables"> + <param format="qza,no_unzip.zip" label="--i-tables: ARTIFACTS... List[FeatureTable[Frequency]] The collection of feature tables to be merged. [required]" name="additional_input" optional="False" type="data" /> + </repeat> + <param label="--p-overlap-method: " name="poverlapmethod" optional="True" type="select"> + <option selected="True" value="None">Selection is Optional</option> + <option value="error_on_overlapping_sample">error_on_overlapping_sample</option> + <option value="error_on_overlapping_feature">error_on_overlapping_feature</option> + <option value="sum">sum</option> + </param> + <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" /> + + </inputs> + + <outputs> + <data format="qza" label="${tool.name} on ${on_string}: mergedtable.qza" name="omergedtable" /> + + </outputs> + + <help><![CDATA[ +Combine multiple tables +############################################################### + +Combines feature tables using the `overlap_method` provided. + +Parameters +---------- +tables : List[FeatureTable[Frequency]] + The collection of feature tables to be merged. +overlap_method : Str % Choices('error_on_overlapping_sample', 'error_on_overlapping_feature', 'sum'), optional + Method for handling overlapping ids. + +Returns +------- +merged_table : FeatureTable[Frequency] + The resulting merged feature table. + ]]></help> + <macros> + <import>qiime_citation.xml</import> + </macros> + <expand macro="qiime_citation"/> +</tool> \ No newline at end of file