Mercurial > repos > ebi-gxa > scanpy_run_pca

comparison scanpy-run-pca.xml @ 12:3e7ede8e1c94 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 13:14:04 +0000
parents 2dd53b944e78
children 988edd5fa902
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11:aee7b7f9cae3 12:3e7ede8e1c94
1 <?xml version="1.0" encoding="utf-8"?> 1 <?xml version="1.0" encoding="utf-8"?>
2 <tool id="scanpy_run_pca" name="Scanpy RunPCA" version="@TOOL_VERSION@+galaxy10" profile="@PROFILE@"> 2 <tool id="scanpy_run_pca" name="Scanpy RunPCA" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
3 <description>for dimensionality reduction</description> 3 <description>for dimensionality reduction</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"/>
54 54
55 </inputs> 55 </inputs>
56 56
57 <outputs> 57 <outputs>
58 <expand macro="output_data_obj" description="PCA object"/> 58 <expand macro="output_data_obj" description="PCA object"/>
59 <data name="output_embed" format="tsv" from_work_dir="embeddings.tsv" label="${tool.name} on ${on_string}: PCA embeddings"> 59 <data name="output_embed" format="tabular" from_work_dir="embeddings.tsv" label="${tool.name} on ${on_string}: PCA embeddings">
60 <filter>extra_outputs and 'embeddings' in extra_outputs.split(',')</filter> 60 <filter>extra_outputs and 'embeddings' in extra_outputs.split(',')</filter>
61 </data> 61 </data>
62 </outputs> 62 </outputs>
63 63
64 <tests> 64 <tests>
68 <param name="output_format" value="anndata"/> 68 <param name="output_format" value="anndata"/>
69 <param name="extra_outputs" value="embeddings"/> 69 <param name="extra_outputs" value="embeddings"/>
70 <param name="n_pcs" value="50"/> 70 <param name="n_pcs" value="50"/>
71 <param name="zero_center" value="true"/> 71 <param name="zero_center" value="true"/>
72 <param name="svd_solver" value="arpack"/> 72 <param name="svd_solver" value="arpack"/>
73 <param name="random_seed" value="0"/> 73 <param name="random_seed" value="1"/>
74 <param name="chunked" value="false"/> 74 <param name="chunked" value="false"/>
75 <output name="output_h5" file="run_pca.h5" ftype="h5" compare="sim_size"/> 75 <output name="output_h5" file="run_pca.h5" ftype="h5" compare="sim_size"/>
76 <output name="output_embed" file="run_pca.embeddings.csv" ftype="csv" compare="sim_size"> 76 <output name="output_embed" file="run_pca.embeddings.tsv" ftype="tabular" compare="sim_size" >
77 <assert_contents> 77 <assert_contents>
78 <has_n_columns n="50" sep=","/> 78 <has_n_columns n="51"/>
79 </assert_contents> 79 </assert_contents>
80 </output> 80 </output>
81 </test> 81 </test>
82 </tests> 82 </tests>
83 83