Mercurial > repos > ebi-gxa > monocle3_partition

comparison monocle3-partition.xml @ 0:be84f9c3a2dd draft

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"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
author ebi-gxa
date Mon, 16 Sep 2019 09:51:42 -0400
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children 92ca41fbc123
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-1:000000000000 0:be84f9c3a2dd
1 <?xml version="1.0" encoding="utf-8"?>
2 <tool id="monocle3_partition" name="Monocle3 partition" version="@TOOL_VERSION@+galaxy0">
3 <description>of cells into groups</description>
4 <macros>
5 <import>monocle3-macros.xml</import>
6 </macros>
7 <expand macro="requirements"/>
8 <command detect_errors="exit_code"><![CDATA[
9 LANG=en_US.UTF-8 monocle3 partition
10 --reduction-method '${reduction_method}'
11 #if $knn
12 --knn '${knn}'
13 #end if
14 #if $weight
15 --weight
16 #end if
17 #if $louvain_iter
18 --louvain-iter '${louvain_iter}'
19 #end if
20 #if $resolution
21 --resolution '${resolution}'
22 #end if
23 #if $partition_qval
24 --partition-qval '${partition_qval}'
25 #end if
26
27 @INPUT_OPTS@
28 @OUTPUT_OPTS@
29
30 @VERBOSE@
31 ]]></command>
32
33 <inputs>
34 <expand macro="input_object_params"/>
35 <expand macro="output_object_params"/>
36 <param name="reduction_method" argument="--reduction-method" type="select" label="The dimensionality reduction to base the clustering on.">
37 <option selected="true" value="UMAP">UMAP</option>
38 <option value="tSNE">tSNE</option>
39 <option value="PCA">PCA</option>
40 <option value="LSI">LSI</option>
41 </param>
42 <param name="knn" argument="--knn" optional="true" type="integer" value="20" label="Number of nearest neighbours used for Louvain clustering."/>
43 <param name="weight" argument="--weight" type="boolean" checked="false" label="When this option is set, calculate the weight for each edge in the kNN graph."/>
44 <param name="louvain_iter" argument="--louvain-iter" optional="true" type="integer" value="1" label="The number of iterations for Louvain clustering."/>
45 <param name="resolution" argument="--resolution" optional="true" type="float" label="Resolution of clustering result, specifying the granularity of clusters. Not used by default and the standard igraph louvain clustering algorithm will be used."/>
46 <param name="partition_qval" argument="--partition-qval" optional="true" type="float" value="0.05" label="The q-value threshold used to determine the partition of cells."/>
47 <expand macro="verbose_flag"/>
48 </inputs>
49
50 <outputs>
51 <data name="output_rds" format="rdata" from_work_dir="output.RDS" label="${tool.name} on ${on_string}: ${output_object_format}"/>
52 </outputs>
53
54 <tests>
55 <test>
56 <param name="input_object_file" value="input.RDS"/>
57 <param name="input_object_format" value="cds3"/>
58 <param name="reduction_method" value="UMAP"/>
59 <param name="knn" value="20"/>
60 <param name="louvain_iter" value="1"/>
61 <param name="partition_qval" value="0.05"/>
62 <param name="output_object_format" value="cds3"/>
63 <output name="output_rds" file="output.rds" ftype="rdata" compare="sim_size"/>
64 </test>
65 </tests>
66
67 <help><![CDATA[
68 ==============================================
69 Monocle3 clustering of cells (`cluster_cells`)
70 ==============================================
71
72 Cluster the primary dimensionality reduced space
73
74 @HELP@
75
76 @VERSION_HISTORY@
77 ]]></help>
78 <expand macro="citations"/>
79 </tool>