Mercurial > repos > ecology > ecoregion_clara_cluster
comparison cluster.xml @ 1:edb8d19735a6 draft
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 459ba1277acd7d8d4a02f90dbd7ff444bf8eac92
| author | ecology |
|---|---|
| date | Wed, 24 Jan 2024 15:53:07 +0000 |
| parents | 32849c52aa54 |
| children | 24a81631a8b5 |
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| 0:32849c52aa54 | 1:edb8d19735a6 |
|---|---|
| 18 '$output1' | 18 '$output1' |
| 19 '$output2' | 19 '$output2' |
| 20 '$output3' | 20 '$output3' |
| 21 ]]></command> | 21 ]]></command> |
| 22 <inputs> | 22 <inputs> |
| 23 <param name="predictionmatrix" type="data" format="tabular" label="Prediction matrix (data to cluster from Cluster Estimate tool) "/> | 23 <param name="envfile" type="data" format="tabular" label="Environmental file (tabular only)"/> |
| 24 <param name="envfile" type="data" format="txt,csv,tabular" label="Environmental file"/> | 24 <param name="predictionmatrix" type="data" format="tabular" label="Prediction matrix (file 'data to cluster' from Cluster Estimate tool)"/> |
| 25 <param name="predictionfile" type="data" format="tabular" label="Prediction file (data.bio table from Cluster Estimate tool)"/> | 25 <param name="predictionfile" type="data" format="tabular" label="Prediction file (file 'data.bio table' from Cluster Estimate tool)"/> |
| 26 <param name="k" type="integer" label="Number of Cluster wanted" min= "1" value="2"/> | 26 <param name="k" type="integer" label="Number of Cluster wanted" min= "1" value="2"/> |
| 27 <param name="metric" type="select" label="What metric to use to calculate dissimilarities between observations ?"> | 27 <param name="metric" type="select" label="What metric to use to calculate dissimilarities between observations ?"> |
| 28 <option value = "manhattan">manhattan</option> | 28 <option value = "manhattan">manhattan</option> |
| 29 <option value = "euclidean">euclidean</option> | 29 <option value = "euclidean">euclidean</option> |
| 30 <option value = "jaccard">jaccard</option> | 30 <option value = "jaccard">jaccard</option> |
| 31 </param> | 31 </param> |
| 32 <param name="sample" type="integer" label= "The number of samples to be drawn from the dataset" min="5" value="10"/> | 32 <param name="sample" type="integer" label= "The number of samples to be drawn from the dataset" min="5" value="10"/> |
| 33 </inputs> | 33 </inputs> |
| 34 <outputs> | 34 <outputs> |
| 35 <data name="output1" from_work_dir="sih.png" format="png" label="SIH plot"/> | 35 <data name="output1" from_work_dir="sih.png" format="png" label="SIH plot"/> |
| 36 <data name="output2" from_work_dir="points_clus.txt" format="txt" label="Cluster points"/> | 36 <data name="output2" from_work_dir="points_clus.tsv" format="tabular" label="Cluster points"/> |
| 37 <data name="output3" from_work_dir="clus.txt" format="txt" label="Cluster info"/> | 37 <data name="output3" from_work_dir="clus.tsv" format="tabular" label="Cluster info"/> |
| 38 </outputs> | 38 </outputs> |
| 39 <tests> | 39 <tests> |
| 40 <test> | 40 <test> |
| 41 <param name="predictionmatrix" value="Data_to_cluster.tsv"/> | 41 <param name="predictionmatrix" value="Data_to_cluster.tsv"/> |
| 42 <param name="envfile" value="ceamarc_env.csv"/> | 42 <param name="envfile" value="ceamarc_env.tsv"/> |
| 43 <param name="predictionfile" value="Data.bio_table.tsv"/> | 43 <param name="predictionfile" value="Data.bio_table.tsv"/> |
| 44 <param name='k' value="2"/> | 44 <param name='k' value="2"/> |
| 45 <param name='metric' value="manhattan"/> | 45 <param name='metric' value="manhattan"/> |
| 46 <param name='sample' value="10"/> | 46 <param name='sample' value="10"/> |
| 47 <output name='output1'> | 47 <output name='output1'> |
| 48 <assert_contents> | 48 <assert_contents> |
| 49 <has_size value="8128" delta="500"/> | 49 <has_size value="7369" delta="1000"/> |
| 50 </assert_contents> | 50 </assert_contents> |
| 51 </output> | 51 </output> |
| 52 <output name='output2'> | 52 <output name='output2'> |
| 53 <assert_contents> | 53 <assert_contents> |
| 54 <has_size value="255" delta="1000" /> | 54 <has_n_columns n="3"/> |
| 55 <has_text text="lat"/> | |
| 55 </assert_contents> | 56 </assert_contents> |
| 56 </output> | 57 </output> |
| 57 <output name='output3' > | 58 <output name='output3' > |
| 58 <assert_contents> | 59 <assert_contents> |
| 59 <has_size value="2008" delta="1000000" /> | 60 <has_size value="2298" delta="50" /> |
| 60 </assert_contents> | 61 </assert_contents> |
| 61 </output> | 62 </output> |
| 62 </test> | 63 </test> |
| 63 </tests> | 64 </tests> |
| 64 <help><![CDATA[ | 65 <help><![CDATA[ |