Mercurial > repos > ebi-gxa > scanpy_run_tsne
comparison scanpy-run-tsne.xml @ 29:abdb61e4afa3 draft default tip
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ee197a80b2d591c393e1662854bc119b2ecab11e-dirty
| author | ebi-gxa |
|---|---|
| date | Tue, 27 Feb 2024 16:43:06 +0000 |
| parents | 64cd33540fee |
| children |
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| 28:64cd33540fee | 29:abdb61e4afa3 |
|---|---|
| 1 <?xml version="1.0" encoding="utf-8"?> | 1 <?xml version="1.0" encoding="utf-8"?> |
| 2 <tool id="scanpy_run_tsne" name="Scanpy RunTSNE" version="@TOOL_VERSION@+galaxy93" profile="@PROFILE@"> | 2 <tool id="scanpy_run_tsne" name="Scanpy RunTSNE" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@"> |
| 3 <description>visualise cell clusters using tSNE</description> | 3 <description>visualise cell clusters using tSNE</description> |
| 4 <macros> | 4 <macros> |
| 5 <import>scanpy_macros2.xml</import> | 5 <import>scanpy_macros2.xml</import> |
| 6 </macros> | 6 </macros> |
| 7 <expand macro="requirements"/> | 7 <expand macro="requirements"/> |
| 98 <param name="output_format" value="anndata"/> | 98 <param name="output_format" value="anndata"/> |
| 99 <param name="default" value="false"/> | 99 <param name="default" value="false"/> |
| 100 <param name="perplexity_file" value="perplexity.txt"/> | 100 <param name="perplexity_file" value="perplexity.txt"/> |
| 101 <param name="embeddings" value="true"/> | 101 <param name="embeddings" value="true"/> |
| 102 <param name="random_seed" value="0"/> | 102 <param name="random_seed" value="0"/> |
| 103 <output name="output_h5" file="run_tsne.h5" ftype="h5" compare="sim_size"/> | 103 <output name="output_h5" ftype="h5"> |
| 104 <output name="output_embed" file="run_tsne.embeddings.tsv" ftype="tabular" compare="sim_size"> | 104 <assert_contents> |
| 105 <has_h5_keys keys="obsm/X_tsne"/> | |
| 106 </assert_contents> | |
| 107 </output> | |
| 108 <output name="output_embed" file="run_tsne.embeddings.tsv" ftype="tabular" compare="sim_size" delta_frac="0.1"> | |
| 105 <assert_contents> | 109 <assert_contents> |
| 106 <has_n_columns n="3"/> | 110 <has_n_columns n="3"/> |
| 107 </assert_contents> | 111 </assert_contents> |
| 108 </output> | 112 </output> |
| 109 </test> | 113 </test> |
| 113 <param name="output_format" value="anndata"/> | 117 <param name="output_format" value="anndata"/> |
| 114 <param name="default" value="false"/> | 118 <param name="default" value="false"/> |
| 115 <param name="perplexity" value="30"/> | 119 <param name="perplexity" value="30"/> |
| 116 <param name="embeddings" value="true"/> | 120 <param name="embeddings" value="true"/> |
| 117 <param name="random_seed" value="0"/> | 121 <param name="random_seed" value="0"/> |
| 118 <output name="output_h5" file="run_tsne.h5" ftype="h5" compare="sim_size"/> | 122 <output name="output_h5" ftype="h5"> |
| 119 <output name="output_embed" file="run_tsne.embeddings.tsv" ftype="tabular" compare="sim_size"> | 123 <assert_contents> |
| 124 <has_h5_keys keys="obsm/X_tsne"/> | |
| 125 </assert_contents> | |
| 126 </output> | |
| 127 <output name="output_embed" file="run_tsne.embeddings.tsv" ftype="tabular" compare="sim_size" delta_frac="0.1"> | |
| 120 <assert_contents> | 128 <assert_contents> |
| 121 <has_n_columns n="3"/> | 129 <has_n_columns n="3"/> |
| 122 </assert_contents> | 130 </assert_contents> |
| 123 </output> | 131 </output> |
| 124 </test> | 132 </test> |