Mercurial > repos > ebi-gxa > scanpy_compute_graph
comparison scanpy-neighbours.xml @ 1:e7fd6981c0f0 draft
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
author | ebi-gxa |
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date | Mon, 16 Sep 2019 08:18:53 -0400 |
parents | 3d242b0d97d0 |
children | 4f9811ccc575 |
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0:3d242b0d97d0 | 1:e7fd6981c0f0 |
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1 <?xml version="1.0" encoding="utf-8"?> | 1 <?xml version="1.0" encoding="utf-8"?> |
2 <tool id="scanpy_compute_graph" name="Scanpy ComputeGraph" version="@TOOL_VERSION@+galaxy1"> | 2 <tool id="scanpy_compute_graph" name="Scanpy ComputeGraph" version="@TOOL_VERSION@+galaxy0"> |
3 <description>to derive kNN graph</description> | 3 <description>to derive kNN graph</description> |
4 <macros> | 4 <macros> |
5 <import>scanpy_macros.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-neighbours.py | 10 PYTHONIOENCODING=utf-8 scanpy-neighbors |
11 -i input.h5 | 11 #if $settings.default == "false" |
12 -f '${input_format}' | 12 --n-neighbors '${settings.n_neighbours}' |
13 -o output.h5 | 13 --method '${settings.method}' |
14 -F '${output_format}' | 14 --random-state '${settings.random_seed}' |
15 #if $settings.default == "false" | 15 #if $settings.use_rep != "auto" |
16 -N '${settings.n_neighbours}' | 16 --use-rep '${settings.use_rep}' |
17 -m '${settings.method}' | |
18 -s '${settings.random_seed}' | |
19 #if $settings.use_rep != "auto" | |
20 -r '${settings.use_rep}' | |
21 #end if | |
22 #if $settings.n_pcs | |
23 -n '${settings.n_pcs}' | |
24 #end if | |
25 #if $settings.knn | |
26 --knn | |
27 #end if | |
28 #if $settings.metric | |
29 -M '${settings.metric}' | |
30 #end if | |
31 #end if | 17 #end if |
18 #if $settings.n_pcs | |
19 --n-pcs '${settings.n_pcs}' | |
20 #end if | |
21 ${settings.knn} | |
22 #end if | |
23 @INPUT_OPTS@ | |
24 @OUTPUT_OPTS@ | |
32 ]]></command> | 25 ]]></command> |
33 | 26 |
34 <inputs> | 27 <inputs> |
35 <expand macro="input_object_params"/> | 28 <expand macro="input_object_params"/> |
36 <expand macro="output_object_params"/> | 29 <expand macro="output_object_params"/> |
37 <conditional name="settings"> | 30 <conditional name="settings"> |
38 <param name="default" type="boolean" checked="true" label="Use programme defaults"/> | 31 <param name="default" type="boolean" checked="true" label="Use programme defaults"/> |
39 <when value="true"/> | 32 <when value="true"/> |
40 <when value="false"> | 33 <when value="false"> |
41 <param name="n_neighbours" argument="--n-neighbors" type="integer" value="15" label="Maximum number of neighbours used"/> | 34 <param name="n_neighbours" argument="--n-neighbors" type="integer" value="15" label="Maximum number of neighbours used"/> |
42 <param name="use_rep" type="select" label="Use the indicated representation"> | 35 <param name="use_rep" type="text" label="Use the indicated representation"> |
43 <option value="X_pca">X_pca, use PCs</option> | 36 <option value="X_pca" selected="true">X_pca, use PCs</option> |
44 <option value="X">X, use normalised expression values</option> | 37 <option value="X">X, use normalised expression values</option> |
45 <option value="auto" selected="true">Automatically chosen based on problem size</option> | |
46 </param> | 38 </param> |
47 <param name="n_pcs" argument="--n-pcs" type="integer" value="50" optional="true" label="Number of PCs to use"/> | 39 <param name="n_pcs" argument="--n-pcs" type="integer" value="50" optional="true" label="Number of PCs to use"/> |
48 <param name="knn" argument="--knn/--no-knn" type="boolean" checked="true" label="Use hard threshold to restrict neighbourhood size (otherwise use a Gaussian kernel to down weight distant neighbours)"/> | 40 <param name="knn" argument="--knn" type="boolean" truevalue="" falsevalue="--no-knn" checked="true" |
41 label="Use hard threshold to restrict neighbourhood size (otherwise use a Gaussian kernel to down weight distant neighbours)"/> | |
49 <param name="method" argument="--method" type="select" label="Method for calculating connectivity"> | 42 <param name="method" argument="--method" type="select" label="Method for calculating connectivity"> |
50 <option value="umap" selected="true">UMAP</option> | 43 <option value="umap" selected="true">UMAP</option> |
51 <option value="gauss">Gaussian</option> | 44 <option value="gauss">Gaussian</option> |
52 </param> | 45 </param> |
53 <param name="metric" argument="--metric" type="text" value="euclidean" label="Distance metric"/> | |
54 <param name="random_seed" argument="--random-seed" type="integer" value="0" label="Seed for random number generator"/> | 46 <param name="random_seed" argument="--random-seed" type="integer" value="0" label="Seed for random number generator"/> |
55 </when> | 47 </when> |
56 </conditional> | 48 </conditional> |
57 </inputs> | 49 </inputs> |
58 | 50 |
69 <param name="n_neighbours" value="15"/> | 61 <param name="n_neighbours" value="15"/> |
70 <param name="n_pcs" value="50"/> | 62 <param name="n_pcs" value="50"/> |
71 <param name="knn" value="true"/> | 63 <param name="knn" value="true"/> |
72 <param name="random_seed" value="0"/> | 64 <param name="random_seed" value="0"/> |
73 <param name="method" value="umap"/> | 65 <param name="method" value="umap"/> |
74 <param name="metric" value="euclidean"/> | |
75 <output name="output_h5" file="compute_graph.h5" ftype="h5" compare="sim_size"/> | 66 <output name="output_h5" file="compute_graph.h5" ftype="h5" compare="sim_size"/> |
76 </test> | 67 </test> |
77 </tests> | 68 </tests> |
78 | 69 |
79 <help><![CDATA[ | 70 <help><![CDATA[ |