Mercurial > repos > florianbegusch > qiime2_all
comparison qiime_metadata_distance-matrix.xml @ 0:09b7bcb72fa7 draft
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| author | florianbegusch |
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| date | Thu, 24 May 2018 02:11:44 -0400 |
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| -1:000000000000 | 0:09b7bcb72fa7 |
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| 1 <?xml version="1.0" ?> | |
| 2 <tool id="qiime_metadata_distance-matrix" name="qiime metadata distance-matrix" version="2018.4"> | |
| 3 <description> - Create a distance matrix from a numeric Metadata column</description> | |
| 4 <requirements> | |
| 5 <requirement type="package" version="2018.4">qiime2</requirement> | |
| 6 </requirements> | |
| 7 <command> | |
| 8 <![CDATA[ | |
| 9 qiime metadata distance-matrix --m-metadata-column="$mmetadatacolumn" | |
| 10 | |
| 11 #def list_dict_to_string(list_dict): | |
| 12 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name') | |
| 13 #for d in list_dict[1:]: | |
| 14 #set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name') | |
| 15 #end for | |
| 16 #return $file_list | |
| 17 #end def | |
| 18 | |
| 19 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile) | |
| 20 #if str($cmdconfig) != 'None': | |
| 21 --cmd-config=$cmdconfig | |
| 22 #end if | |
| 23 --o-distance-matrix=odistancematrix; | |
| 24 cp odistancematrix.qza $odistancematrix; | |
| 25 ]]> | |
| 26 </command> | |
| 27 <inputs> | |
| 28 <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file"> | |
| 29 <param label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [required]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" /> | |
| 30 </repeat> | |
| 31 <param label="--m-metadata-column: MetadataColumn[Numeric] Column from metadata file or artifact viewable as metadata. Numeric metadata column to compute pairwise Euclidean distances from [required]" name="mmetadatacolumn" optional="False" type="text"/> | |
| 32 | |
| 33 <param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/> | |
| 34 </inputs> | |
| 35 <outputs> | |
| 36 <data format="qza" label="${tool.name} on ${on_string}: distance-matrix.qza" name="odistancematrix"/> | |
| 37 </outputs> | |
| 38 <help> | |
| 39 <![CDATA[ | |
| 40 Create a distance matrix from a numeric Metadata column | |
| 41 -------------------------------------------------------- | |
| 42 | |
| 43 Create a distance matrix from a numeric metadata column. The Euclidean | |
| 44 distance is computed between each pair of samples or features in the | |
| 45 column. Tip: the distance matrix produced by this method can be used as | |
| 46 input to the Mantel test available in `q2-diversity`. | |
| 47 | |
| 48 Parameters | |
| 49 ---------- | |
| 50 metadata : MetadataColumn[Numeric] | |
| 51 Numeric metadata column to compute pairwise Euclidean distances from | |
| 52 | |
| 53 Returns | |
| 54 ------- | |
| 55 distance_matrix : DistanceMatrix | |
| 56 \ | |
| 57 ]]> | |
| 58 </help> | |
| 59 </tool> |