Mercurial > repos > florianbegusch > qiime2_suite
comparison qiime2/qiime_gneiss_gradient-clustering.xml @ 9:f190567fe3f6 draft
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author | florianbegusch |
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date | Wed, 14 Aug 2019 15:12:48 -0400 |
parents | 51025741f326 |
children | a0a8d77a991c |
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8:d66c7509e8f9 | 9:f190567fe3f6 |
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1 <?xml version="1.0" ?> | 1 <?xml version="1.0" ?> |
2 <tool id="qiime_gneiss_gradient-clustering" name="qiime gneiss gradient-clustering" version="2019.4"> | 2 <tool id="qiime_gneiss_gradient-clustering" name="qiime gneiss gradient-clustering" version="2019.7"> |
3 <description> - Hierarchical clustering using gradient information.</description> | 3 <description> - Hierarchical clustering using gradient information.</description> |
4 <requirements> | 4 <requirements> |
5 <requirement type="package" version="2019.4">qiime2</requirement> | 5 <requirement type="package" version="2019.7">qiime2</requirement> |
6 </requirements> | 6 </requirements> |
7 <command><![CDATA[ | 7 <command><![CDATA[ |
8 qiime gneiss gradient-clustering | 8 qiime gneiss gradient-clustering |
9 | 9 |
10 --i-table=$itable | 10 --i-table=$itable |
11 --m-gradient-column="$mgradientcolumn" | 11 --m-gradient-column="$mgradientcolumn" |
12 | 12 |
13 | 13 |
14 #if $input_files_mgradientfile: | 14 #if $mgradientfile: |
15 #def list_dict_to_string(list_dict): | 15 --m-gradient-file=$mgradientfile |
16 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name') | |
17 #for d in list_dict[1:]: | |
18 #set $file_list = $file_list + ',' + d['additional_input'].__getattr__('file_name') | |
19 #end for | |
20 #return $file_list | |
21 #end def | |
22 --m-gradient-file=$list_dict_to_string($input_files_mgradientfile) | |
23 #end if | 16 #end if |
24 | 17 |
25 #if $pnoweighted: | 18 #if $pnoweighted: |
26 --p-no-weighted | 19 --p-no-weighted |
27 #end if | 20 #end if |
33 <inputs> | 26 <inputs> |
34 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency | RelativeFrequency | Composition] The feature table containing the samples in which the columns will be clustered. [required]" name="itable" optional="False" type="data"/> | 27 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency | RelativeFrequency | Composition] The feature table containing the samples in which the columns will be clustered. [required]" name="itable" optional="False" type="data"/> |
35 <param label="--m-gradient-column: COLUMN MetadataColumn[Numeric] Contains gradient values to sort the features and samples. [required]" name="mgradientcolumn" optional="False" type="text"/> | 28 <param label="--m-gradient-column: COLUMN MetadataColumn[Numeric] Contains gradient values to sort the features and samples. [required]" name="mgradientcolumn" optional="False" type="text"/> |
36 <param label="--p-no-weighted : Specifies if abundance or presence/absence information should be used to perform the clustering. [default: False]" name="pnoweighted" selected="False" type="boolean"/> | 29 <param label="--p-no-weighted : Specifies if abundance or presence/absence information should be used to perform the clustering. [default: False]" name="pnoweighted" selected="False" type="boolean"/> |
37 | 30 |
38 <repeat name="input_files_mgradientfile" optional="False" title="--m-gradient-file"> | 31 <param label="--m-gradient-file: " name="mgradientfile" optional="True" type="data" format="tabular,qza,no_unzip.zip" /> |
39 <param label="--m-gradient-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" /> | |
40 </repeat> | |
41 | 32 |
42 </inputs> | 33 </inputs> |
43 <outputs> | 34 <outputs> |
44 <data format="qza" label="${tool.name} on ${on_string}: clustering.qza" name="oclustering"/> | 35 <data format="qza" label="${tool.name} on ${on_string}: clustering.qza" name="oclustering"/> |
45 </outputs> | 36 </outputs> |