Mercurial > repos > ebi-gxa > scanpy_run_diffmap

comparison scanpy-run-diffmap.xml @ 0:34d65f2ccde3 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 08:26:37 -0400
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children 47603f46d6d9
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-1:000000000000 0:34d65f2ccde3
1 <?xml version="1.0" encoding="utf-8"?>
2 <tool id="scanpy_run_diffmap" name="Scanpy DiffusionMap" version="@TOOL_VERSION@+galaxy0">
3 <description>calculate diffusion components</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 embed diffmap
11 --n-comps ${n_comps}
12 #if $use_graph
13 --use-graph '${use_graph}'
14 #end if
15 #if $key_added
16 --key-added '${key_added}'
17 #end if
18 $export_embed
19 @INPUT_OPTS@
20 @OUTPUT_OPTS@
21 ]]></command>
22
23 <inputs>
24 <expand macro="input_object_params"/>
25 <expand macro="output_object_params"/>
26
27 <param name="n_comps" argument="--n-comps" type="integer" min="2" value="10"
28 label="Number of diffusion components to calculate"/>
29 <param name="export_embed" argument="--export-embedding" type="boolean" checked="false"
30 truevalue="--export-embedding embed.tsv" falsevalue=""
31 label="Export embeddings as a tab-separated text table"/>
32 <param name="use_graph" argument="--use-graph" value="neighbors" type="text"
33 label="Name of the slot that holds the KNN graph"/>
34 <param name="key_added" argument="--key-added" type="text" optional="true"
35 label="Additional suffix to the name of the slot to save the calculated trajectory"/>
36 </inputs>
37
38 <outputs>
39 <data name="output_h5" format="h5" from_work_dir="output.h5" label="${tool.name} on ${on_string}: diffmap object"/>
40 <data name="output_embed" format="tsv" from_work_dir="embed.tsv" label="${tool.name} on ${on_string}: diffmap embedding">
41 <filter>export_embed</filter>
42 </data>
43 </outputs>
44
45 <tests>
46 <test>
47 <param name="input_obj_file" value="diffmap.h5"/>
48 <param name="input_format" value="anndata"/>
49 <param name="output_format" value="anndata"/>
50 <param name="n_dcs" value="10"/>
51 <param name="root_attr" value="leiden"/>
52 <param name="root_value" value="1"/>
53 <param name="use_graph" value="neighbors"/>
54 <output name="output_h5" file="paga.h5" ftype="h5" compare="sim_size"/>
55 </test>
56 </tests>
57
58 <help><![CDATA[
59 ====================================================
60 Calculate Diffusion Components (`scanpy.tl.diffmap`)
61 ====================================================
62
63 Calculate diffusion components from single cell KNN graphs.
64
65 This requires to run `Scanpy ComputeGraph`, first.
66
67 It yields `X_diffmap`, the dimension-reduced representation in diffusion
68 components space.
69
70 @HELP@
71
72 @VERSION_HISTORY@
73 ]]></help>
74 <expand macro="citations">
75 <citation type="doi">10.1186/s13059-019-1663-x</citation>
76 </expand>
77 </tool>