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comparison scanpy-neighbours.xml @ 0:3d242b0d97d0 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 9bf9a6e46a330890be932f60d1d996dd166426c4
author ebi-gxa
date Wed, 03 Apr 2019 11:11:14 -0400
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-1:000000000000 0:3d242b0d97d0
1 <?xml version="1.0" encoding="utf-8"?>
2 <tool id="scanpy_compute_graph" name="Scanpy ComputeGraph" version="@TOOL_VERSION@+galaxy1">
3 <description>to derive kNN graph</description>
4 <macros>
5 <import>scanpy_macros.xml</import>
6 </macros>
7 <expand macro="requirements"/>
8 <command detect_errors="exit_code"><![CDATA[
9 ln -s '${input_obj_file}' input.h5 &&
10 PYTHONIOENCODING=utf-8 scanpy-neighbours.py
11 -i input.h5
12 -f '${input_format}'
13 -o output.h5
14 -F '${output_format}'
15 #if $settings.default == "false"
16 -N '${settings.n_neighbours}'
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
32 ]]></command>
33
34 <inputs>
35 <expand macro="input_object_params"/>
36 <expand macro="output_object_params"/>
37 <conditional name="settings">
38 <param name="default" type="boolean" checked="true" label="Use programme defaults"/>
39 <when value="true"/>
40 <when value="false">
41 <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">
43 <option value="X_pca">X_pca, use PCs</option>
44 <option value="X">X, use normalised expression values</option>
45 <option value="auto" selected="true">Automatically chosen based on problem size</option>
46 </param>
47 <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)"/>
49 <param name="method" argument="--method" type="select" label="Method for calculating connectivity">
50 <option value="umap" selected="true">UMAP</option>
51 <option value="gauss">Gaussian</option>
52 </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"/>
55 </when>
56 </conditional>
57 </inputs>
58
59 <outputs>
60 <data name="output_h5" format="h5" from_work_dir="output.h5" label="${tool.name} on ${on_string}: Graph object"/>
61 </outputs>
62
63 <tests>
64 <test>
65 <param name="input_obj_file" value="run_pca.h5"/>
66 <param name="input_format" value="anndata"/>
67 <param name="output_format" value="anndata"/>
68 <param name="default" value="false"/>
69 <param name="n_neighbours" value="15"/>
70 <param name="n_pcs" value="50"/>
71 <param name="knn" value="true"/>
72 <param name="random_seed" value="0"/>
73 <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"/>
76 </test>
77 </tests>
78
79 <help><![CDATA[
80 =============================================================
81 Compute a neighborhood graph of observations (`pp.neighbors`)
82 =============================================================
83
84 The neighbor search efficiency of this heavily relies on UMAP (McInnes et al, 2018),
85 which also provides a method for estimating connectivities of data points -
86 the connectivity of the manifold (`method=='umap'`). If `method=='diffmap'`,
87 connectivities are computed according to Coifman et al (2005), in the adaption of
88 Haghverdi et al (2016).
89
90 @HELP@
91
92 @VERSION_HISTORY@
93 ]]></help>
94 <expand macro="citations"/>
95 </tool>