Mercurial > repos > ebi-gxa > scanpy_run_tsne

comparison scanpy-run-tsne.xml @ 29:abdb61e4afa3 draft default tip

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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>