Mercurial > repos > florianbegusch > qiime2_all
comparison qiime_diversity_alpha-group-significance.xml @ 0:09b7bcb72fa7 draft
Uploaded
| author | florianbegusch |
|---|---|
| date | Thu, 24 May 2018 02:11:44 -0400 |
| parents | |
| children |
comparison
equal
deleted
inserted
replaced
| -1:000000000000 | 0:09b7bcb72fa7 |
|---|---|
| 1 <?xml version="1.0" ?> | |
| 2 <tool id="qiime_diversity_alpha-group-significance" name="qiime diversity alpha-group-significance" version="2018.4"> | |
| 3 <description> - Alpha diversity comparisons</description> | |
| 4 <requirements> | |
| 5 <requirement type="package" version="2018.4">qiime2</requirement> | |
| 6 </requirements> | |
| 7 <command><![CDATA[ | |
| 8 qiime diversity alpha-group-significance | |
| 9 #def list_dict_to_string(list_dict): | |
| 10 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name') | |
| 11 #for d in list_dict[1:]: | |
| 12 #set $file_list = $file_list + ',' + d['additional_input'].__getattr__('file_name') | |
| 13 #end for | |
| 14 #return $file_list | |
| 15 #end def | |
| 16 | |
| 17 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile) --i-alpha-diversity=$ialphadiversity | |
| 18 | |
| 19 #if str($cmdconfig) != 'None': | |
| 20 --cmd-config=$cmdconfig | |
| 21 #end if | |
| 22 | |
| 23 --o-visualization=ovisualization; | |
| 24 qiime tools export ovisualization.qzv --output-dir out && mkdir -p '$ovisualization.files_path' | |
| 25 && cp -r out/* '$ovisualization.files_path' | |
| 26 && mv '$ovisualization.files_path/index.html' '$ovisualization'; | |
| 27 ]]></command> | |
| 28 <inputs> | |
| 29 <param format="qza,no_unzip.zip" label="--i-alpha-diversity: SampleData[AlphaDiversity] Vector of alpha diversity values by sample. [required]" name="ialphadiversity" optional="False" type="data"/> | |
| 30 <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file"> | |
| 31 <param label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. The sample metadata. [required]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" /> | |
| 32 </repeat> | |
| 33 <param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/> | |
| 34 </inputs> | |
| 35 <outputs> | |
| 36 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/> | |
| 37 </outputs> | |
| 38 <help><![CDATA[ | |
| 39 Alpha diversity comparisons | |
| 40 ---------------------------- | |
| 41 | |
| 42 Visually and statistically compare groups of alpha diversity values. | |
| 43 | |
| 44 Parameters | |
| 45 ---------- | |
| 46 alpha_diversity : SampleData[AlphaDiversity] | |
| 47 Vector of alpha diversity values by sample. | |
| 48 metadata : Metadata | |
| 49 The sample metadata. | |
| 50 | |
| 51 Returns | |
| 52 ------- | |
| 53 visualization : Visualization | |
| 54 \ | |
| 55 ]]> | |
| 56 </help> | |
| 57 </tool> |