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comparison scanpy-run-dpt.xml @ 0:f57f57c459d8 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 08:24:32 -0400
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children 34f674af79ff
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-1:000000000000 0:f57f57c459d8
1 <?xml version="1.0" encoding="utf-8"?>
2 <tool id="scanpy_run_dpt" name="Scanpy DPT" version="@TOOL_VERSION@+galaxy0">
3 <description>diffusion pseudotime inference</description>
4 <macros>
5 <import>scanpy_macros2.xml</import>
6 </macros>
7 <expand macro="requirements"/>
8 <command detect_errors="exit_code"><![CDATA[
9 ln -s '${input_obj_file}' input.h5 &&
10 PYTHONIOENCODING=utf-8 scanpy-cli dpt
11 --n-dcs $n_dcs
12 --root '${root_attr}' '${root_value}'
13 #if $n_branchings > 0
14 --n-branchings ${n_branchings}
15 --min-group-size ${min_group_size}
16 #end if
17 #if $use_graph
18 --use-graph '${use_graph}'
19 #end if
20 #if $key_added
21 --key-added '${key_added}'
22 #end if
23 @INPUT_OPTS@
24 @OUTPUT_OPTS@
25 ]]></command>
26
27 <inputs>
28 <expand macro="input_object_params"/>
29 <expand macro="output_object_params"/>
30
31 <param name="n_dcs" argument="--n-dcs" type="integer" min="2" value="10"
32 label="Number of diffusion components to use"/>
33 <param name="n_branchings" argument="--n-branchings" min="0" type="integer" value="0"
34 label="Number of branchings to detect"/>
35 <param name="min_group_size" argument="--min-group-size" type="float" min="0" max="1" value="0"
36 label="The fraction of total cells under which further splitting is skipped during recursive splitting of branches"
37 help="Ignored when `Number of branchings to detect` is 0"/>
38 <param name="root_attr" argument="--root {attr} value" type="text"
39 label="Name of attribute that defines clustering"/>
40 <param name="root_value" argument="--root attr {value}" type="text"
41 label="Name of the clustering that defines the root cell type"/>
42 <param name="use_graph" argument="--use-graph" value="neighbors" type="text"
43 label="Name of the slot that holds the KNN graph"/>
44 <param name="key_added" argument="--key-added" type="text" optional="true"
45 label="Additional suffix to the name of the slot to save the calculated trajectory"/>
46 </inputs>
47
48 <outputs>
49 <data name="output_h5" format="h5" from_work_dir="output.h5" label="${tool.name} on ${on_string}: dpt object"/>
50 </outputs>
51
52 <tests>
53 <test>
54 <param name="input_obj_file" value="diffmap.h5"/>
55 <param name="input_format" value="anndata"/>
56 <param name="output_format" value="anndata"/>
57 <param name="n_dcs" value="10"/>
58 <param name="root_attr" value="leiden"/>
59 <param name="root_value" value="1"/>
60 <param name="use_graph" value="neighbors"/>
61 <output name="output_h5" file="paga.h5" ftype="h5" compare="sim_size"/>
62 </test>
63 </tests>
64
65 <help><![CDATA[
66 ================================================
67 Calculate Diffusion Pseudotime (`scanpy.tl.dpt`)
68 ================================================
69
70 Calculate diffusion pseudotime from single cell KNN graphs.
71
72 This requires to run `Scanpy DiffusionMap` and `Scanpy FindCluster`, first.
73
74 It yields `dpt_pseudotime`, diffusion pseudotime as an attribute for each cell.
75
76 @HELP@
77
78 @VERSION_HISTORY@
79 ]]></help>
80 <expand macro="citations">
81 <citation type="doi">10.1186/s13059-019-1663-x</citation>
82 </expand>
83 </tool>