Mercurial > repos > ebi-gxa > scanpy_run_tsne

comparison scanpy-run-tsne.xml @ 12:dccd544c21ca draft

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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 62f47287c7e8449c59a1f1f454852ddc669b1b1e-dirty"
author ebi-gxa
date Mon, 07 Sep 2020 14:01:11 +0000
parents e61ba8b05578
children b5e1939cc155
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11:a597590ccf6c 12:dccd544c21ca
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@+galaxy10" 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"/>
13 #end if 13 #end if
14 #if $key_added 14 #if $key_added
15 --key-added '${key_added}' 15 --key-added '${key_added}'
16 #end if 16 #end if
17 #if $embeddings 17 #if $embeddings
18 --export-embedding embeddings.csv 18 --export-embedding embeddings.tsv
19 #end if 19 #end if
20 #if $settings.default == "false" 20 #if $settings.default == "false"
21 #if $settings.perplexity_file 21 #if $settings.perplexity_file
22 --perplexity \$( cat $settings.perplexity_file ) 22 --perplexity \$( cat $settings.perplexity_file )
23 #else 23 #else
44 ]]></command> 44 ]]></command>
45 45
46 <inputs> 46 <inputs>
47 <expand macro="input_object_params"/> 47 <expand macro="input_object_params"/>
48 <expand macro="output_object_params"/> 48 <expand macro="output_object_params"/>
49 <param name="embeddings" type="boolean" checked="true" label="Output embeddings in csv format"/> 49 <param name="embeddings" type="boolean" checked="true" label="Output embeddings in tsv format"/>
50 50
51 <param name="use_rep" argument="--use-rep" type="select" label="Use the indicated representation"> 51 <param name="use_rep" argument="--use-rep" type="select" label="Use the indicated representation">
52 <option value="X_pca">X_pca, use PCs</option> 52 <option value="X_pca">X_pca, use PCs</option>
53 <option value="X">X, use normalised expression values</option> 53 <option value="X">X, use normalised expression values</option>
54 <option value="auto" selected="true">Automatically chosen based on problem size</option> 54 <option value="auto" selected="true">Automatically chosen based on problem size</option>
73 73
74 </inputs> 74 </inputs>
75 75
76 <outputs> 76 <outputs>
77 <expand macro="output_data_obj" description="tSNE object"/> 77 <expand macro="output_data_obj" description="tSNE object"/>
78 <data name="output_embed" format="csv" from_work_dir="embeddings.csv" label="${tool.name} on ${on_string}: tSNE embeddings"> 78 <data name="output_embed" format="tabular" from_work_dir="embeddings.tsv" label="${tool.name} on ${on_string}: tSNE embeddings">
79 <filter>embeddings</filter> 79 <filter>embeddings</filter>
80 </data> 80 </data>
81 </outputs> 81 </outputs>
82 82
83 <tests> 83 <tests>
87 <param name="output_format" value="anndata"/> 87 <param name="output_format" value="anndata"/>
88 <param name="default" value="false"/> 88 <param name="default" value="false"/>
89 <param name="embeddings" value="true"/> 89 <param name="embeddings" value="true"/>
90 <param name="random_seed" value="0"/> 90 <param name="random_seed" value="0"/>
91 <output name="output_h5" file="run_tsne.h5" ftype="h5" compare="sim_size"/> 91 <output name="output_h5" file="run_tsne.h5" ftype="h5" compare="sim_size"/>
92 <output name="output_embed" file="run_tsne.embeddings.csv" ftype="csv" compare="sim_size"> 92 <output name="output_embed" file="run_tsne.embeddings.tsv" ftype="tabular" compare="sim_size">
93 <assert_contents> 93 <assert_contents>
94 <has_n_columns n="2" sep=","/> 94 <has_n_columns n="3"/>
95 </assert_contents> 95 </assert_contents>
96 </output> 96 </output>
97 </test> 97 </test>
98 </tests> 98 </tests>
99 99