Mercurial > repos > ebi-gxa > scanpy_run_umap

comparison scanpy-run-umap.xml @ 12:f53bb2c1fa07 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 14:00:37 +0000
parents b282c349bd67
children 135e8cacb57e
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11:10893b1647ff 12:f53bb2c1fa07
1 <?xml version="1.0" encoding="utf-8"?> 1 <?xml version="1.0" encoding="utf-8"?>
2 <tool id="scanpy_run_umap" name="Scanpy RunUMAP" version="@TOOL_VERSION@+galaxy10" profile="@PROFILE@"> 2 <tool id="scanpy_run_umap" name="Scanpy RunUMAP" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
3 <description>visualise cell clusters using UMAP</description> 3 <description>visualise cell clusters using UMAP</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"/>
8 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
9 ln -s '${input_obj_file}' input.h5 && 9 ln -s '${input_obj_file}' input.h5 &&
10 PYTHONIOENCODING=utf-8 scanpy-run-umap 10 PYTHONIOENCODING=utf-8 scanpy-run-umap
11 --use-graph '${use_graph}' 11 --neighbors-key '${use_graph}'
12 --key-added '${key_added}' 12 --key-added '${key_added}'
13 #if $embeddings 13 #if $embeddings
14 --export-embedding embeddings.csv 14 --export-embedding embeddings.tsv
15 #end if 15 #end if
16 #if $settings.default == "false" 16 #if $settings.default == "false"
17 --n-components ${settings.n_components} 17 --n-components ${settings.n_components}
18 --min-dist ${settings.min_dist} 18 --min-dist ${settings.min_dist}
19 --spread ${settings.spread} 19 --spread ${settings.spread}
34 ]]></command> 34 ]]></command>
35 35
36 <inputs> 36 <inputs>
37 <expand macro="input_object_params"/> 37 <expand macro="input_object_params"/>
38 <expand macro="output_object_params"/> 38 <expand macro="output_object_params"/>
39 <param name="embeddings" type="boolean" checked="true" label="Output embeddings in csv format"/> 39 <param name="embeddings" type="boolean" checked="true" label="Output embeddings in tsv format"/>
40 <param name="use_graph" argument="--use-graph" value="neighbors" type="text" 40 <param name="use_graph" argument="--neighbors-key" value="neighbors" type="text"
41 label="Name of the slot that holds the KNN graph"/> 41 label="Name of the slot that holds the KNN graph"/>
42 <param name="key_added" argument="--key-added" type="text" optional="true" 42 <param name="key_added" argument="--key-added" type="text" optional="true"
43 label="Additional suffix to the name of the slot to save the embedding"/> 43 label="Additional suffix to the name of the slot to save the embedding"/>
44 44
45 <conditional name="settings"> 45 <conditional name="settings">
63 </conditional> 63 </conditional>
64 </inputs> 64 </inputs>
65 65
66 <outputs> 66 <outputs>
67 <expand macro="output_data_obj" description="UMAP object"/> 67 <expand macro="output_data_obj" description="UMAP object"/>
68 <data name="output_embed" format="csv" from_work_dir="embeddings.csv" label="${tool.name} on ${on_string}: UMAP embeddings"> 68 <data name="output_embed" format="tabular" from_work_dir="embeddings.tsv" label="${tool.name} on ${on_string}: UMAP embeddings">
69 <filter>embeddings</filter> 69 <filter>embeddings</filter>
70 </data> 70 </data>
71 </outputs> 71 </outputs>
72 72
73 <tests> 73 <tests>
77 <param name="output_format" value="anndata"/> 77 <param name="output_format" value="anndata"/>
78 <param name="default" value="false"/> 78 <param name="default" value="false"/>
79 <param name="embeddings" value="true"/> 79 <param name="embeddings" value="true"/>
80 <param name="random_seed" value="0"/> 80 <param name="random_seed" value="0"/>
81 <output name="output_h5" file="run_umap.h5" ftype="h5" compare="sim_size"/> 81 <output name="output_h5" file="run_umap.h5" ftype="h5" compare="sim_size"/>
82 <output name="output_embed" file="run_umap.embeddings.csv" ftype="csv" compare="sim_size"> 82 <output name="output_embed" file="run_umap.embeddings.tsv" ftype="tabular" compare="sim_size">
83 <assert_contents> 83 <assert_contents>
84 <has_n_columns n="2" sep=","/> 84 <has_n_columns n="3"/>
85 </assert_contents> 85 </assert_contents>
86 </output> 86 </output>
87 </test> 87 </test>
88 </tests> 88 </tests>
89 89