Mercurial > repos > ebi-gxa > scanpy_compute_graph
comparison scanpy-neighbours.xml @ 13:e6c989a9211c draft
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit e572b5425460d57f1bd13ab6374674c1c6801ab3-dirty"
author | ebi-gxa |
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date | Thu, 24 Sep 2020 13:26:39 +0000 |
parents | c78c930e3263 |
children | a57b128ea4f6 |
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12:c78c930e3263 | 13:e6c989a9211c |
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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@+galaxy0" profile="@PROFILE@"> | 2 <tool id="scanpy_compute_graph" name="Scanpy ComputeGraph" version="@TOOL_VERSION@+galaxy1" 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 #from pathlib import Path | |
10 #if $settings.n_neighbors_file | |
11 #set n_neighbors = Path($settings.n_neighbors_file.__str__).read_text().strip() | |
12 #elif $settings.n_neighbors | |
13 #set n_neighbors = $settings.n_neighbors.__str__.strip() | |
14 #end if | |
15 | |
9 ln -s '${input_obj_file}' input.h5 && | 16 ln -s '${input_obj_file}' input.h5 && |
10 PYTHONIOENCODING=utf-8 scanpy-neighbors | 17 PYTHONIOENCODING=utf-8 scanpy-neighbors |
11 #if $settings.default == "false" | 18 #if $settings.default == "false" |
12 #if $settings.n_neighbors_file | 19 #if $n_neighbors |
13 --n-neighbors \$( cat $settings.n_neighbors_file ) | 20 --n-neighbors $n_neighbors |
14 #elif $settings.n_neighbors | |
15 --n-neighbors '${settings.n_neighbors}' | |
16 #end if | 21 #end if |
22 #if $settings.key_added | |
23 #set key_added = $settings.key_added | |
24 #if $n_neighbors | |
25 #set key_added = $key_added.replace('N_NEIGHBORS', $n_neighbors.__str__) | |
26 #end if | |
27 --key-added '${key_added}' | |
28 #end if | |
29 | |
17 --method '${settings.method}' | 30 --method '${settings.method}' |
18 --metric '${settings.metric}' | 31 --metric '${settings.metric}' |
19 --random-state '${settings.random_seed}' | 32 --random-state '${settings.random_seed}' |
20 #if $settings.use_rep != "auto" | 33 #if $settings.use_rep != "auto" |
21 --use-rep '${settings.use_rep}' | 34 --use-rep '${settings.use_rep}' |
34 <expand macro="output_object_params"/> | 47 <expand macro="output_object_params"/> |
35 <conditional name="settings"> | 48 <conditional name="settings"> |
36 <param name="default" type="boolean" checked="true" label="Use programme defaults"/> | 49 <param name="default" type="boolean" checked="true" label="Use programme defaults"/> |
37 <when value="true"/> | 50 <when value="true"/> |
38 <when value="false"> | 51 <when value="false"> |
52 <param name="key_added" argument="--key-added" type="text" optional="true" label="Key added" | |
53 help="If not specified, the neighbors data is stored in .uns[‘neighbors’], distances and connectivities are stored in .obsp[‘distances’] and .obsp[‘connectivities’] respectively. If specified, the neighbors data is added to .uns[key_added], distances are stored in .obsp[key_added+’_distances’] and connectivities in .obsp[key_added+’_connectivities’]." value='neighbours' /> | |
39 <param name="n_neighbors" argument="--n-neighbors" type="integer" value="15" label="Maximum number of neighbors used"/> | 54 <param name="n_neighbors" argument="--n-neighbors" type="integer" value="15" label="Maximum number of neighbors used"/> |
40 <param name="n_neighbors_file" argument="--n-neighbors" type="data" format="txt,tsv" optional="true" | 55 <param name="n_neighbors_file" argument="--n-neighbors" type="data" format="txt,tsv" optional="true" |
41 label="File with n_neighbours, use with parameter iterator. Overrides the n_neighbors setting"/> | 56 label="File with n_neighbours, use with parameter iterator. Overrides the n_neighbors setting"/> |
42 <param name="use_rep" type="select" label="Use the indicated representation"> | 57 <param name="use_rep" type="select" label="Use the indicated representation"> |
43 <option value="X_pca" selected="true">X_pca, use PCs</option> | 58 <option value="X_pca" selected="true">X_pca, use PCs</option> |