Mercurial > repos > ebi-gxa > monocle3_ordercells

comparison monocle3-orderCells.xml @ 0:5520da33a868 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 09:52:31 -0400
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children f58c4eb5446d
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-1:000000000000 0:5520da33a868
1 <?xml version="1.0" encoding="utf-8"?>
2 <tool id="monocle3_orderCells" name="Monocle3 orderCells" version="@TOOL_VERSION@+galaxy0">
3 <description>along trajectories</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 orderCells
10 --reduction-method '${reduction_method}'
11 #if $root_pr_nodes
12 --root-pr-nodes '${root_pr_nodes}'
13 #end if
14 #if $root_cells
15 --root-cells '${root_cells}'
16 #end if
17 #if $cell_phenotype
18 --cell-phenotype '${cell_phenotype}'
19 #end if
20 #if $root_type
21 --root-type '${root_type}'
22 #end if
23
24 @INPUT_OPTS@
25 @OUTPUT_OPTS@
26
27 @VERBOSE@
28 ]]></command>
29
30 <inputs>
31 <expand macro="input_object_params"/>
32 <expand macro="output_object_params"/>
33 <param name="root_pr_nodes" argument="--root-pr-nodes" type="text" optional="true" label="The starting principal points. We learn a principal graph that passes through the middle of the data points and use it to represent the developmental process. Exclusive with the root cell option."/>
34 <param name="root_cells" argument="--root-cells" type="text" optional="true" label="The starting cells. Each cell corresponds to a principal point and multiple cells can correspond to the same principal point. Exclusive with the root node option."/>
35 <param name="cell_phenotype" argument="--cell-phenotype" type="text" optional="true" label="The cell phenotype (column in pdata) used to identify root principal nodes."/>
36 <param name="root_type" argument="--root-type" type="text" optional="true" label="The value in the cell phenotype column used to extract root nodes."/>
37 <param name="reduction_method" argument="--reduction-method" type="select" label="The dimensionality reduction that was used for clustering.">
38 <option selected="true" value="UMAP">UMAP</option>
39 <option value="tSNE">tSNE</option>
40 <option value="PCA">PCA</option>
41 <option value="LSI">LSI</option>
42 </param>
43 <expand macro="verbose_flag"/>
44 </inputs>
45
46 <outputs>
47 <data name="output_rds" format="rdata" from_work_dir="output.RDS" label="${tool.name} on ${on_string}: ${output_object_format}"/>
48 </outputs>
49
50 <tests>
51 <test>
52 <param name="input_object_file" value="input.RDS"/>
53 <param name="input_object_format" value="cds3"/>
54 <param name="reduction_method" value="UMAP"/>
55 <param name="cell_phenotype" value="embryo.time.bin"/>
56 <param name="root_type" value="130-170"/>
57 <param name="output_object_format" value="cds3"/>
58 <output name="output_rds" file="output.rds" ftype="rdata" compare="sim_size"/>
59 </test>
60 </tests>
61
62 <help><![CDATA[
63 ==========================================
64 Monocle3 ordering of cells (`order_cells`)
65 ==========================================
66
67 Order cells using the inferred graph
68
69 @HELP@
70
71 @VERSION_HISTORY@
72 ]]></help>
73 <expand macro="citations"/>
74 </tool>