Mercurial > repos > ebi-gxa > monocle3_plotcells

annotate monocle3-plotCells.xml @ 0:896359db6339 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"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 09:51:16 -0400
parents
children ad64e2d368d6
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
896359db6339 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
1 <?xml version="1.0" encoding="utf-8"?>
896359db6339 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
2 <tool id="monocle3_plotCells" name="Monocle3 plotCells" version="@TOOL_VERSION@+galaxy0">
896359db6339 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
3 <description> in the reduced dimensionality space</description>
896359db6339 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
4 <macros>
896359db6339 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
5 <import>monocle3-macros.xml</import>
896359db6339 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
6 </macros>
896359db6339 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
7 <expand macro="requirements"/>
896359db6339 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
8 <command detect_errors="exit_code"><![CDATA[
896359db6339 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
9 LANG=en_US.UTF-8 monocle3 plotCells
896359db6339 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
10 --reduction-method '$(reduction_method)'
896359db6339 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
11 --norm-method '$(norm_method)'
896359db6339 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
12 #if $xdim
896359db6339 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
13 --xdim '$(xdim)'
896359db6339 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
14 #end if
896359db6339 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
15 #if $ydim
896359db6339 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
16 --ydim '$(ydim)'
896359db6339 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
17 #end if
896359db6339 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
18 #if $color_cells_by
896359db6339 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
19 --color-cells-by '$(color_cells_by)'
896359db6339 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
20 #end if
896359db6339 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
21 #if $genes
896359db6339 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
22 --genes '$(genes)'
896359db6339 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
23 #end if
896359db6339 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
24 #if $cell_size
896359db6339 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
25 --cell-size '$(cell_size)'
896359db6339 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
26 #end if
896359db6339 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
27 #if $alpha
896359db6339 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
28 --alpha '$(alpha)'
896359db6339 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
29 #end if
896359db6339 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
30 #if $label_cell_groups
896359db6339 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
31 --label-cell-groups
896359db6339 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
32 #end if
896359db6339 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
33 #if $no_trajectory_graph
896359db6339 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
34 --no-trajectory-graph
896359db6339 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
35 #end if
896359db6339 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
36 #if $label_groups_by_cluster
896359db6339 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
37 --label-groups-by-cluster
896359db6339 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
38 #end if
896359db6339 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
39 #if $label_leaves
896359db6339 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
40 --label-leaves
896359db6339 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
41 #end if
896359db6339 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
42 #if $label_roots
896359db6339 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
43 --label-roots
896359db6339 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
44 #end if
896359db6339 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
45 #if $label_branch_points
896359db6339 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
46 --label-branch-points
896359db6339 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
47 #end if
896359db6339 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
48
896359db6339 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
49 @INPUT_OPTS@
896359db6339 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
50 output.png
896359db6339 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
51
896359db6339 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
52 @VERBOSE@
896359db6339 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
53 ]]></command>
896359db6339 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
54
896359db6339 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
55 <inputs>
896359db6339 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
56 <expand macro="input_object_params"/>
896359db6339 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
57 <param name="xdim" argument="--xdim" optional="true" type="integer" value="1" label="The column of reducedDimS(cds) to plot on the horizontal axis."/>
896359db6339 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
58 <param name="ydim" argument="--ydim" optional="true" type="integer" value="2" label="The column of reducedDimS(cds) to plot on the vertical axis."/>
896359db6339 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
59 <param name="reduction_method" argument="--reduction-method" type="select" label="The dimensionality reduction for plotting.">
896359db6339 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
60 <option value="UMAP" selected="true">UMAP</option>
896359db6339 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
61 <option value="tSNE">tSNE</option>
896359db6339 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
62 <option value="PCA">PCA</option>
896359db6339 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
63 <option value="LSI">LSI</option>
896359db6339 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
64 </param>
896359db6339 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
65 <param name="color_cells_by" argument="--color-cells-by" optional="true" type="text" value="pseudotime" label="The cell attribute (e.g. the column of pData(cds)) to map to each cell's color, or one of {cluster, partition, pseudotime}."/>
896359db6339 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
66 <param name="genes" argument="--genes" optional="true" type="text" label="A list of gene IDs/short names to plot, one per panel."/>
896359db6339 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
67 <param name="norm_method" argument="--norm-method" type="select" label="Determines how to transform expression values for plotting.">
896359db6339 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
68 <option value="log" selected="true">Size factor correction and log transformation</option>
896359db6339 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
69 <option value="size_only">Size factor correction only</option>
896359db6339 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
70 </param>
896359db6339 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
71 <param name="cell_size" argument="--cell-size" optional="true" type="float" value="1.5" label="The size of the point for each cell."/>
896359db6339 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
72 <param name="alpha" argument="--alpha" optional="true" type="float" value="1" label="The alpha aesthetics for the original cell points, useful to highlight the learned principal graph."/>
896359db6339 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
73 <param name="label_cell_groups" argument="--label-cell-groups" type="boolean" checked="true" label="If set, display the cell group names directly on the plot. Otherwise include a color legend on the side of the plot."/>
896359db6339 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
74 <param name="no_trajectory_graph" argument="--no-trajectory-graph" type="boolean" checked="false" label="When this option is set, skip displaying the trajectory graph inferred by learn_graph()."/>
896359db6339 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
75 <param name="label_groups_by_cluster" argument="--label-groups-by-cluster" type="boolean" checked="false" label="If set, and setting --color-cells-by to something other than cluster, label the cells of each cluster independently. Can result in duplicate labels being present in the manifold."/>
896359db6339 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
76 <param name="label_leaves" argument="--label-leaves" type="boolean" checked="false" label="If set, label the leaves of the principal graph."/>
896359db6339 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
77 <param name="label_roots" argument="--label-roots" type="boolean" checked="false" label="If set, label the roots of the principal graph."/>
896359db6339 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
78 <param name="label_branch_points" argument="--label-branch-points" type="boolean" checked="false" label="If set, label the branch points of the principal graph."/>
896359db6339 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
79 <expand macro="verbose_flag"/>
896359db6339 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
80 </inputs>
896359db6339 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
81
896359db6339 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
82 <outputs>
896359db6339 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
83 <data name="output_tsv" format="png" from_work_dir="output.png" label="${tool.name} on ${on_string}: png"/>
896359db6339 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
84 </outputs>
896359db6339 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
85
896359db6339 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
86 <tests>
896359db6339 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
87 <test>
896359db6339 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
88 <param name="input_object_file" value="input.RDS"/>
896359db6339 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
89 <param name="input_object_format" value="cds3"/>
896359db6339 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
90 <param name="reduction_method" value="UMAP"/>
896359db6339 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
91 <param name="xdim" value="1"/>
896359db6339 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
92 <param name="ydim" value="2"/>
896359db6339 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
93 <param name="color_cells_by" value="pseudotime"/>
896359db6339 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
94 <param name="norm_method" value="log"/>
896359db6339 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
95 <param name="cell_size" value="1.5"/>
896359db6339 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
96 <param name="alpha" value="1"/>
896359db6339 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
97 <output name="output_tsv" file="output.tsv" ftype="tsv" compare="sim_size"/>
896359db6339 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
98 </test>
896359db6339 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
99 </tests>
896359db6339 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
100
896359db6339 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
101 <help><![CDATA[
896359db6339 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
102 =====================================
896359db6339 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
103 Monocle3 cell plotting (`plot_cells`)
896359db6339 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
104 =====================================
896359db6339 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
105
896359db6339 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
106 Display various information about cells (clustering, pseudotime, the inferred graph,
896359db6339 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
107 user-provided annotations, gene expression) in reduced dimensions.
896359db6339 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
108
896359db6339 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
109 @HELP@
896359db6339 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
110
896359db6339 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
111 @VERSION_HISTORY@
896359db6339 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
112 ]]></help>
896359db6339 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
113 <expand macro="citations"/>
896359db6339 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
114 </tool>