Mercurial > repos > iuc > trinity_define_clusters_by_cutting_tree
comparison define_clusters_by_cutting_tree.xml @ 3:b99f4e461291 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit bc4ea54f0deec4ddec8e6cf79fd547491e165686
| author | iuc |
|---|---|
| date | Mon, 28 Aug 2017 16:55:25 -0400 |
| parents | cd71eff81169 |
| children | 75e332bfe023 |
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| 2:cd71eff81169 | 3:b99f4e461291 |
|---|---|
| 3 <macros> | 3 <macros> |
| 4 <import>macros.xml</import> | 4 <import>macros.xml</import> |
| 5 </macros> | 5 </macros> |
| 6 <expand macro="requirements"> | 6 <expand macro="requirements"> |
| 7 <requirement type="package" version="2.34.0">bioconductor-biobase</requirement> | 7 <requirement type="package" version="2.34.0">bioconductor-biobase</requirement> |
| 8 <requirement type="package" version="2.0.6">r-cluster</requirement> | |
| 8 </expand> | 9 </expand> |
| 9 <command detect_errors="aggressive"><![CDATA[ | 10 <command detect_errors="aggressive"><![CDATA[ |
| 10 | 11 |
| 11 define_clusters_by_cutting_tree.pl | 12 define_clusters_by_cutting_tree.pl |
| 12 | 13 |
| 43 <param name="ktree" type="integer" argument="--Ktree" value="2" label="Cut tree into K clusters "/> | 44 <param name="ktree" type="integer" argument="--Ktree" value="2" label="Cut tree into K clusters "/> |
| 44 </when> | 45 </when> |
| 45 <when value="-K"> | 46 <when value="-K"> |
| 46 <param name="k" type="integer" argument="-K" value="2" label="Define K clusters via k-means algorithm" help="This does not leverage the already hierarchically clustered genes, and instead uses a least-sum-of-squares method to define exactly k gene clusters."/> | 47 <param name="k" type="integer" argument="-K" value="2" label="Define K clusters via k-means algorithm" help="This does not leverage the already hierarchically clustered genes, and instead uses a least-sum-of-squares method to define exactly k gene clusters."/> |
| 47 </when> | 48 </when> |
| 48 </conditional> | 49 </conditional> |
| 49 <section name="additional_params" title="Additional Options" expanded="False"> | 50 <section name="additional_params" title="Additional Options" expanded="False"> |
| 50 <param name="column_ordering" type="select" label="Column ordering in expression matrices" argument="--no_column_reordering / --lexical_column_ordering"> | 51 <param name="column_ordering" type="select" label="Column ordering in expression matrices" argument="--no_column_reordering / --lexical_column_ordering"> |
| 51 <option value="">Order based on sample clustering</option> | 52 <option value="">Order based on sample clustering</option> |
| 52 <option value="--no_column_reordering">No reordering based on sample clustering</option> | 53 <option value="--no_column_reordering">No reordering based on sample clustering</option> |
| 53 <option value="--lexical_column_ordering">Reorder column names according to lexical ordering</option> | 54 <option value="--lexical_column_ordering">Reorder column names according to lexical ordering</option> |