Mercurial > repos > florianbegusch > qiime2_wrappers
diff qiime2/qiime_feature-table_merge.xml @ 0:51b9b6b57732 draft
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author | florianbegusch |
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date | Thu, 24 May 2018 05:21:07 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_feature-table_merge.xml Thu May 24 05:21:07 2018 -0400 @@ -0,0 +1,73 @@ +<?xml version="1.0" ?> +<tool id="qiime_feature-table_merge" name="qiime feature-table merge" version="2018.4"> + <description> - Combine multiple tables</description> + <requirements> + <requirement type="package" version="2018.4">qiime2</requirement> + </requirements> + <command> + <![CDATA[ + qiime feature-table merge + + #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($input_files_itables) + + #if str($cmdconfig) != 'None': + --cmd-config=$cmdconfig + #end if + --o-merged-table=omergedtable + #if str($poverlapmethod) != 'None': + --p-overlap-method=$poverlapmethod + #end if + ; + cp omergedtable.qza $omergedtable; + ]]> + </command> + <inputs> + <repeat name="input_files_itables" optional="False" title="--i-tables"> + <param format="qza,no_unzip.zip" label="--i-tables: PATH List[FeatureTable[Frequency]] The collection of feature tables to be merged. [required]" name="additional_input" type="data"/> + </repeat> + <param label="--p-overlap-method: Method for handling overlapping ids. + [default: error_on_overlapping_sample]" name="poverlapmethod" optional="True" type="select"> + <option selected="True" value="None">Selection is Optional</option> + <option value="error_on_overlapping_feature">error_on_overlapping_feature</option> + <option value="error_on_overlapping_sample">error_on_overlapping_sample</option> + <option value="sum">sum</option> + </param> + <param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/> + </inputs> + <outputs> + <data format="qza" label="${tool.name} on ${on_string}: merged-table.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_feature', 'error_on_overlapping_sample', '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>