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comparison scanpy-find-cluster.xml @ 1:ee181563bae7 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 4846776f55931e176f7e77af7c185ec6fec7d142"
author ebi-gxa
date Mon, 16 Sep 2019 08:13:51 -0400
parents ce27ae8a36cd
children d5290f98fde4
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0:ce27ae8a36cd 1:ee181563bae7
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>