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comparison scanpy-find-markers.xml @ 0:c608fd80ec15 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 9bf9a6e46a330890be932f60d1d996dd166426c4
author ebi-gxa
date Wed, 03 Apr 2019 11:08:46 -0400
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children 71668dd2d47b
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-1:000000000000 0:c608fd80ec15
1 <?xml version="1.0" encoding="utf-8"?>
2 <tool id="scanpy_find_markers" name="Scanpy FindMarkers" version="@TOOL_VERSION@+galaxy1">
3 <description>to find differentially expressed genes between groups</description>
4 <macros>
5 <import>scanpy_macros.xml</import>
6 </macros>
7 <expand macro="requirements"/>
8 <command detect_errors="exit_code"><![CDATA[
9 ln -s '${input_obj_file}' input.h5 &&
10 PYTHONIOENCODING=utf-8 scanpy-find-markers.py
11 -i input.h5
12 -f '${input_format}'
13 -o output.h5
14 -F '${output_format}'
15 -n '${n_genes}'
16 #if $output_markers
17 --output-text-file output.csv
18 #end if
19 #if $settings.default == "false"
20 -g '${settings.groupby}'
21 --reference '${settings.reference}'
22 --method '${settings.method}'
23 #if $settings.use_raw == "false"
24 --no-raw
25 #end if
26 #if $settings.rankby_abs
27 --rankby_abs
28 #end if
29 #if $settings.groups
30 --groups '${settings.groups}'
31 #end if
32 #end if
33 ]]></command>
34
35 <inputs>
36 <expand macro="input_object_params"/>
37 <expand macro="output_object_params"/>
38 <param name="n_genes" argument="--n-genes" type="integer" value="50" label="Number of top genes to show per group/cluster"/>
39 <param name="output_markers" type="boolean" checked="true" label="Output markers table in csv format"/>
40 <conditional name="settings">
41 <param name="default" type="boolean" checked="true" label="Use programme defaults"/>
42 <when value="true"/>
43 <when value="false">
44 <param name="groupby" argument="--groupby" type="text" value="louvain" label="The sample grouping/clustering to use."/>
45 <param name="use_raw" type="boolean" checked="true" label="Use raw attribute if present"/>
46 <param name="reference" argument="--reference" type="text" value="rest" label="If 'rest', compare to the union of the rest of the group/cluster. If a group identifier, compare to that group"/>
47 <param name="method" argument="--method" type="select" label="Method for testing differentially expressed genes">
48 <option value="t-test_overestim_var" selected="true">t-test with over-estimated variance</option>
49 <option value="t-test">t-test</option>
50 <option value="wilcoxon">wilcoxon test, currently broken don't use</option>
51 <option value="logreg">logistic regression</option>
52 </param>
53 <param name="rankby_abs" argument="--rankby_abs" type="boolean" checked="false" label="Rank by absolute value of the scores instead of the scores"/>
54 <param name="groups" argument="--groups" optional="true" type="text" label="Subset of groups/clusters to which comparisons shell be restricted."/>
55 </when>
56 </conditional>
57 </inputs>
58
59 <outputs>
60 <data name="output_h5" format="h5" from_work_dir="output.h5" label="${tool.name} on ${on_string}: Marker object"/>
61 <data name="output_csv" format="csv" from_work_dir="output.csv" label="${tool.name} on ${on_string}: Marker table">
62 <filter>output_markers</filter>
63 </data>
64 </outputs>
65
66 <tests>
67 <test>
68 <param name="input_obj_file" value="find_cluster.h5"/>
69 <param name="input_format" value="anndata"/>
70 <param name="output_format" value="anndata"/>
71 <param name="output_csv" value="true"/>
72 <param name="n_genes" value="50"/>
73 <param name="output_markers" value="false"/>
74 <param name="default" value="false"/>
75 <param name="groupby" value="louvain"/>
76 <param name="method" value="t-test_overestim_var"/>
77 <param name="rankby_abs" value="false"/>
78 <output name="output_h5" file="find_markers.h5" ftype="h5" compare="sim_size"/>
79 </test>
80 </tests>
81
82 <help><![CDATA[
83 =============================================================
84 Rank genes for characterizing groups (`tl.rank_genes_groups`)
85 =============================================================
86
87 Rank genes for characterizing groups.
88
89 @HELP@
90
91 @VERSION_HISTORY@
92 ]]></help>
93 <expand macro="citations"/>
94 </tool>