Mercurial > repos > ebi-gxa > seurat_run_pca
comparison seurat_run_pca.xml @ 5:9547ebb03f6f draft
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 355bb52d2e9d170b1db237e649657cc14e0a047a"
| author | ebi-gxa |
|---|---|
| date | Fri, 04 Mar 2022 07:29:26 +0000 |
| parents | 3fd59cdcb477 |
| children |
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| 4:3fd59cdcb477 | 5:9547ebb03f6f |
|---|---|
| 1 <tool id="seurat_run_pca" name="Seurat RunPCA" version="@SEURAT_VERSION@+galaxy0"> | 1 <tool id="seurat_run_pca" name="Seurat RunPCA" profile="18.01" version="@SEURAT_VERSION@+galaxy0"> |
| 2 <description>run a PCA dimensionality reduction</description> | 2 <description>run a PCA dimensionality reduction</description> |
| 3 <macros> | 3 <macros> |
| 4 <import>seurat_macros.xml</import> | 4 <import>seurat_macros.xml</import> |
| 5 </macros> | 5 </macros> |
| 6 <expand macro="requirements" /> | 6 <expand macro="requirements" /> |
| 44 <data name="output_sdev" format="csv" from_work_dir="output_sdev" label="${tool.name} on ${on_string}: Seurat Std dev"/> | 44 <data name="output_sdev" format="csv" from_work_dir="output_sdev" label="${tool.name} on ${on_string}: Seurat Std dev"/> |
| 45 </outputs> | 45 </outputs> |
| 46 | 46 |
| 47 <tests> | 47 <tests> |
| 48 <test> | 48 <test> |
| 49 <param name="rds_seurat_file" ftype="rdata" value="scaled_seurat.rds"/> | 49 <param name="rds_seurat_file" ftype="rdata" value="E-MTAB-6077-3k_features_90_cells-scaled.rds"/> |
| 50 <output name="rds_seurat_file" ftype="rdata" value="pca_seurat.rds" compare="sim_size" delta="10000000"/> | 50 <output name="rds_seurat_file" ftype="rdata"> |
| 51 <output name="output_embed" value="pca_embeddings.csv" compare="sim_size" delta="10000000" /> | 51 <assert_contents> |
| 52 <output name="output_load" value="pca_loadings.csv" compare="sim_size" delta="10000000" /> | 52 <has_size value="5052296" delta="200000"/> |
| 53 <output name="output_sdev" value="pca_stdev.txt" compare="sim_size" delta="10000000" /> | 53 </assert_contents> |
| 54 </output> | |
| 55 <output name="output_embed" > | |
| 56 <assert_contents> | |
| 57 <has_n_lines n="92"/> | |
| 58 </assert_contents> | |
| 59 </output> | |
| 60 <output name="output_load" > | |
| 61 <assert_contents> | |
| 62 <has_n_lines n="2001"/> | |
| 63 </assert_contents> | |
| 64 </output> | |
| 65 <output name="output_sdev" > | |
| 66 <assert_contents> | |
| 67 <has_n_lines n="50"/> | |
| 68 </assert_contents> | |
| 69 </output> | |
| 54 </test> | 70 </test> |
| 55 </tests> | 71 </tests> |
| 56 <help><![CDATA[ | 72 <help><![CDATA[ |
| 57 .. class:: infomark | 73 .. class:: infomark |
| 58 | 74 |