Mercurial > repos > ebi-gxa > scanpy_find_cluster
comparison scanpy-find-cluster.xml @ 1:ee181563bae7 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 08:13:51 -0400 |
parents | ce27ae8a36cd |
children | d5290f98fde4 |
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0:ce27ae8a36cd | 1:ee181563bae7 |
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1 <?xml version="1.0" encoding="utf-8"?> | 1 <?xml version="1.0" encoding="utf-8"?> |
2 <tool id="scanpy_find_cluster" name="Scanpy FindCluster" version="@TOOL_VERSION@+galaxy1"> | 2 <tool id="scanpy_find_cluster" name="Scanpy FindCluster" version="@TOOL_VERSION@+galaxy1"> |
3 <description>based on community detection on KNN graph</description> | 3 <description>based on community detection on 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-find-cluster.py | 10 PYTHONIOENCODING=utf-8 scanpy-find-cluster |
11 -i input.h5 | 11 ${method} |
12 -f '${input_format}' | 12 #if $settings.default == "false" |
13 -o output.h5 | 13 --use-graph '${settings.use_graph}' |
14 -F '${output_format}' | 14 #if $settings.key_added |
15 #if $output_cluster | 15 --key-added '${settings.key_added}' |
16 --output-text-file output.tsv | |
17 #end if | 16 #end if |
18 #if $settings.default == "false" | 17 #if $settings.resolution_file |
19 --flavor '${settings.flavor}' | 18 --resolution \$( cat $settings.resolution_file ) |
20 --key-added '${settings.key_added}' | 19 #elif $settings.resolution |
21 -s '${settings.random_seed}' | 20 --resolution '${settings.resolution}' |
22 #if $settings.flavor == "vtraag" and $settings.resolution_file | |
23 --resolution \$( cat $settings.resolution_file ) | |
24 #elif $settings.flavor == "vtraag" | |
25 --resolution '${settings.resolution}' | |
26 #end if | |
27 #if $settings.restrict_to | |
28 --restrict-to '${settings.restrict_to}' | |
29 #end if | |
30 #if $settings.use_weights | |
31 --use-weights | |
32 #end if | |
33 #end if | 21 #end if |
22 #if $settings.restrict_to | |
23 --restrict-to '${settings.restrict_to}' | |
24 #end if | |
25 #if $settings.use_weights | |
26 --use-weights | |
27 #end if | |
28 --random-state '${settings.random_seed}' | |
29 ${settings.directed} | |
30 #end if | |
31 #if $output_cluster | |
32 --export-cluster output.tsv | |
33 #end if | |
34 @INPUT_OPTS@ | |
35 @OUTPUT_OPTS@ | |
34 ]]></command> | 36 ]]></command> |
35 | 37 |
36 <inputs> | 38 <inputs> |
37 <expand macro="input_object_params"/> | 39 <expand macro="input_object_params"/> |
38 <expand macro="output_object_params"/> | 40 <expand macro="output_object_params"/> |
39 <param name="output_cluster" type="boolean" checked="true" label="Output cluster in two column text format"/> | 41 <param name="output_cluster" type="boolean" checked="true" label="Output cluster in two column text format"/> |
42 | |
43 <param name="method" type="select" label="Clustering algorithm"> | |
44 <option value="louvain" selected="true">Louvain</option> | |
45 <option value="leiden">Leiden</option> | |
46 </param> | |
47 | |
40 <conditional name="settings"> | 48 <conditional name="settings"> |
41 <param name="default" type="boolean" checked="true" label="Use programme defaults"/> | 49 <param name="default" type="boolean" checked="true" label="Use programme defaults"/> |
42 <when value="true"/> | 50 <when value="true"/> |
43 <when value="false"> | 51 <when value="false"> |
44 <param name="flavor" argument="--flavor" type="select" label="Use the indicated representation"> | 52 <param name="use_graph" argument="--use-graph" value="neighbors" type="text" |
45 <option value="vtraag" selected="true">vtraag</option> | 53 label="Name of the slot that holds the KNN graph"/> |
46 <option value="igraph">igraph</option> | 54 <param name="key_added" argument="--key-added" type="text" optional="true" |
47 </param> | 55 label="Additional suffix to the name of the slot to save the calculated trajectory"/> |
48 <param name="resolution" argument="--resolution" type="float" value="1.0" label="Resolution, high value for more and smaller clusters"/> | 56 |
49 <param name="resolution_file" argument="--resolution" type="data" format="txt,tsv" optional="true" label="File with resolution, use with parameter iterator. Overrides the resolution setting"/> | 57 <param name="resolution" argument="--resolution" type="float" min="0.0" value="1.0" |
50 <param name="restrict_to" argument="--restrict-to" type="text" optional="true" label="Restrict clustering to certain sample categories"/> | 58 label="Resolution, high value for more and smaller clusters"/> |
51 <param name="key_added" argument="--key-added" type="text" value="louvain" label="Key under which to add the cluster labels (do not change unless you know what you are doing)"/> | 59 <param name="resolution_file" argument="--resolution" type="data" format="txt,tsv" optional="true" |
60 label="File with resolution, use with parameter iterator. Overrides the resolution setting"/> | |
61 <param name="restrict_to" argument="--restrict-to" type="text" optional="true" | |
62 label="Restrict clustering to certain sample categories"/> | |
52 <param name="use_weights" argument="--use-weights" type="boolean" checked="false" label="Use weights from knn graph"/> | 63 <param name="use_weights" argument="--use-weights" type="boolean" checked="false" label="Use weights from knn graph"/> |
53 <param name="random_seed" argument="--random-seed" type="integer" value="0" label="Seed for random number generator"/> | 64 <param name="random_seed" argument="--random-seed" type="integer" value="0" label="Seed for random number generator"/> |
65 <param name="directed" argument="--directed" type="boolean" truevalue="--directed" falsevalue="--undirected" checked="true" | |
66 label="Interpret the adjacency matrix as directed graph."/> | |
54 </when> | 67 </when> |
55 </conditional> | 68 </conditional> |
56 </inputs> | 69 </inputs> |
57 | 70 |
58 <outputs> | 71 <outputs> |
67 <param name="input_obj_file" value="compute_graph.h5"/> | 80 <param name="input_obj_file" value="compute_graph.h5"/> |
68 <param name="input_format" value="anndata"/> | 81 <param name="input_format" value="anndata"/> |
69 <param name="output_format" value="anndata"/> | 82 <param name="output_format" value="anndata"/> |
70 <param name="output_txt" value="true"/> | 83 <param name="output_txt" value="true"/> |
71 <param name="default" value="false"/> | 84 <param name="default" value="false"/> |
72 <param name="flavor" value="vtraag"/> | |
73 <param name="resolution" value="1.0"/> | 85 <param name="resolution" value="1.0"/> |
74 <param name="random_seed" value="0"/> | 86 <param name="random_seed" value="0"/> |
75 <output name="output_h5" file="find_cluster.h5" ftype="h5" compare="sim_size"/> | 87 <output name="output_h5" file="find_cluster.h5" ftype="h5" compare="sim_size"/> |
76 <output name="output_txt" file="find_cluster.tsv" ftype="tsv"/> | 88 <output name="output_txt" file="find_cluster.tsv" ftype="tsv"/> |
77 </test> | 89 </test> |
78 </tests> | 90 </tests> |
79 | 91 |
80 <help><![CDATA[ | 92 <help><![CDATA[ |
81 =========================================== | 93 ====================================================================== |
82 Cluster cells into subgroups (`tl.louvain`) | 94 Cluster cells into subgroups (`scanpy.tl.louvain`, `scanpy.tl.leiden`) |
83 =========================================== | 95 ====================================================================== |
84 | 96 |
85 Cluster cells using the Louvain algorithm (Blondel et al, 2008) in the implementation | 97 Cluster cells using the Louvain algorithm (Blondel et al, 2008) in the |
86 of Traag et al,2017. The Louvain algorithm has been proposed for single-cell | 98 implementation of Traag et al, 2017, or the Leiden algorithm (Traag et al, |
87 analysis by Levine et al, 2015. | 99 2019). The Louvain algorithm has been proposed for single-cell analysis by |
100 Levine et al, 2015. | |
88 | 101 |
89 This requires to run `Scanpy ComputeGraph`, first. | 102 This requires to run `Scanpy ComputeGraph`, first. |
90 | 103 |
91 It yields `louvain`, generated cluster label. | 104 It by default yields `louvain` or `leiden`, generated cluster label. |
92 | 105 |
93 @HELP@ | 106 @HELP@ |
94 | 107 |
95 @VERSION_HISTORY@ | 108 @VERSION_HISTORY@ |
96 ]]></help> | 109 ]]></help> |
97 <expand macro="citations"> | 110 <expand macro="citations"> |
98 <citation type="doi">10.1088/1742-5468/2008/10/P10008</citation> | 111 <citation type="doi">10.1088/1742-5468/2008/10/P10008</citation> |
99 <citation type="doi">10.1016/j.cell.2015.05.047</citation> | 112 <citation type="doi">10.1016/j.cell.2015.05.047</citation> |
113 <citation type="doi">10.1038/s41598-019-41695-z</citation> | |
100 <citation type="doi">10.5281/zenodo.35117</citation> | 114 <citation type="doi">10.5281/zenodo.35117</citation> |
101 </expand> | 115 </expand> |
102 </tool> | 116 </tool> |