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comparison scanpy-run-paga.xml @ 0:3e53344e540d 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 08:25:36 -0400
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1 <?xml version="1.0" encoding="utf-8"?>
2 <tool id="scanpy_run_paga" name="Scanpy PAGA" version="@TOOL_VERSION@+galaxy0">
3 <description>trajectory 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 '${input_obj_file}' input.h5 &&
10 PYTHONIOENCODING=utf-8 scanpy-cli paga
11 --groups '${groups}'
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 @INPUT_OPTS@
19 @OUTPUT_OPTS@
20 ]]></command>
21
22 <inputs>
23 <expand macro="input_object_params"/>
24 <expand macro="output_object_params"/>
25
26 <param name="groups" argument="--groups" type="text" label="Name of the clustering"/>
27 <param name="use_graph" argument="--use-graph" value="neighbors" type="text" label="Name of the slot that holds the KNN graph"/>
28 <param name="key_added" argument="--key-added" type="text" optional="true" label="Additional suffix to the name of the slot to save the calculated trajectory"/>
29 </inputs>
30
31 <outputs>
32 <data name="output_h5" format="h5" from_work_dir="output.h5" label="${tool.name} on ${on_string}: PAGA object"/>
33 </outputs>
34
35 <tests>
36 <test>
37 <param name="input_obj_file" value="compute_graph.h5"/>
38 <param name="input_format" value="anndata"/>
39 <param name="output_format" value="anndata"/>
40 <param name="groups" value="leiden"/>
41 <param name="use_graph" value="neighbors"/>
42 <output name="output_h5" file="paga.h5" ftype="h5" compare="sim_size"/>
43 </test>
44 </tests>
45
46 <help><![CDATA[
47 ===================================================================
48 Perform PAGA (partition-based graph abstraction) (`scanpy.tl.paga`)
49 ===================================================================
50
51 Infer trajectories by mapping out the coarse-grained connectivity structures of
52 complex manifolds of single cell KNN graphs (Wolf et al, 2019).
53
54 This requires to run `Scanpy FindCluster`, first.
55
56 It yields `paga`, connectivity graph between clusters.
57
58 @HELP@
59
60 @VERSION_HISTORY@
61 ]]></help>
62 <expand macro="citations">
63 <citation type="doi">10.1186/s13059-019-1663-x</citation>
64 </expand>
65 </tool>