Mercurial > repos > ebi-gxa > scanpy_compute_graph

comparison scanpy-neighbours.xml @ 11:232937b5bb8f 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 121972f836fc6f5a60390abcdc1e2fe904b79072"
author ebi-gxa
date Fri, 05 Jun 2020 09:12:59 -0400
parents c938bef2ca98
children c78c930e3263
comparison
equal deleted inserted replaced
10:3bce5710a90b 11:232937b5bb8f
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@+galaxy10" profile="@PROFILE@"> 2 <tool id="scanpy_compute_graph" name="Scanpy ComputeGraph" version="@TOOL_VERSION@+galaxy11" profile="@PROFILE@">
3 <description>to derive kNN graph</description> 3 <description>to derive kNN graph</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-neighbors 10 PYTHONIOENCODING=utf-8 scanpy-neighbors
11 #if $settings.default == "false" 11 #if $settings.default == "false"
12 --n-neighbors '${settings.n_neighbours}' 12 #if $settings.n_neighbors_file
13 --n-neighbors \$( cat $settings.n_neighbors_file )
14 #elif $settings.n_neighbors
15 --n-neighbors '${settings.n_neighbors}'
16 #end if
13 --method '${settings.method}' 17 --method '${settings.method}'
14 --random-state '${settings.random_seed}' 18 --random-state '${settings.random_seed}'
15 #if $settings.use_rep != "auto" 19 #if $settings.use_rep != "auto"
16 --use-rep '${settings.use_rep}' 20 --use-rep '${settings.use_rep}'
17 #end if 21 #end if
29 <expand macro="output_object_params"/> 33 <expand macro="output_object_params"/>
30 <conditional name="settings"> 34 <conditional name="settings">
31 <param name="default" type="boolean" checked="true" label="Use programme defaults"/> 35 <param name="default" type="boolean" checked="true" label="Use programme defaults"/>
32 <when value="true"/> 36 <when value="true"/>
33 <when value="false"> 37 <when value="false">
34 <param name="n_neighbours" argument="--n-neighbors" type="integer" value="15" label="Maximum number of neighbours used"/> 38 <param name="n_neighbors" argument="--n-neighbors" type="integer" value="15" label="Maximum number of neighbors used"/>
39 <param name="n_neighbors_file" argument="--n-neighbors" type="data" format="txt,tsv" optional="true"
40 label="File with n_neighbours, use with parameter iterator. Overrides the n_neighbors setting"/>
35 <param name="use_rep" type="text" label="Use the indicated representation"> 41 <param name="use_rep" type="text" label="Use the indicated representation">
36 <option value="X_pca" selected="true">X_pca, use PCs</option> 42 <option value="X_pca" selected="true">X_pca, use PCs</option>
37 <option value="X">X, use normalised expression values</option> 43 <option value="X">X, use normalised expression values</option>
38 </param> 44 </param>
39 <param name="n_pcs" argument="--n-pcs" type="integer" value="50" optional="true" label="Number of PCs to use"/> 45 <param name="n_pcs" argument="--n-pcs" type="integer" value="50" optional="true" label="Number of PCs to use"/>
40 <param name="knn" argument="--knn" type="boolean" truevalue="" falsevalue="--no-knn" checked="true" 46 <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)"/> 47 label="Use hard threshold to restrict neighbourhood size (otherwise use a Gaussian kernel to down weight distant neighbors)"/>
42 <param name="method" argument="--method" type="select" label="Method for calculating connectivity"> 48 <param name="method" argument="--method" type="select" label="Method for calculating connectivity">
43 <option value="umap" selected="true">UMAP</option> 49 <option value="umap" selected="true">UMAP</option>
44 <option value="gauss">Gaussian</option> 50 <option value="gauss">Gaussian</option>
45 </param> 51 </param>
46 <param name="random_seed" argument="--random-seed" type="integer" value="0" label="Seed for random number generator"/> 52 <param name="random_seed" argument="--random-seed" type="integer" value="0" label="Seed for random number generator"/>
56 <test> 62 <test>
57 <param name="input_obj_file" value="run_pca.h5"/> 63 <param name="input_obj_file" value="run_pca.h5"/>
58 <param name="input_format" value="anndata"/> 64 <param name="input_format" value="anndata"/>
59 <param name="output_format" value="anndata"/> 65 <param name="output_format" value="anndata"/>
60 <param name="default" value="false"/> 66 <param name="default" value="false"/>
61 <param name="n_neighbours" value="15"/> 67 <param name="n_neighbors" value="15"/>
62 <param name="n_pcs" value="50"/> 68 <param name="n_pcs" value="50"/>
63 <param name="knn" value="true"/> 69 <param name="knn" value="true"/>
64 <param name="random_seed" value="0"/> 70 <param name="random_seed" value="0"/>
65 <param name="method" value="umap"/> 71 <param name="method" value="umap"/>
66 <output name="output_h5" file="compute_graph.h5" ftype="h5" compare="sim_size"/> 72 <output name="output_h5" file="compute_graph.h5" ftype="h5" compare="sim_size"/>