Mercurial > repos > ebi-gxa > monocle3_topmarkers

comparison monocle3-topmarkers.xml @ 0:bc2df96ef963 draft

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"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c388aa3bb719eff471508b6f01cae8583ee7bb1d"
author ebi-gxa
date Thu, 14 May 2020 17:17:27 -0400
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1 <?xml version="1.0" encoding="utf-8"?>
2 <tool id="monocle3_topmarkers" name="Monocle3 top markers" version="0.1.5+galaxy0" profile="@PROFILE@">
3 <description>for cell groups</description>
4 <macros>
5 <import>monocle3-macros.xml</import>
6 </macros>
7 <requirements>
8 <requirement type="package" version="0.0.8">monocle3-cli</requirement>
9 </requirements>
10 <command detect_errors="exit_code"><![CDATA[
11 ln -s '$input_object' input.rds;
12 #if $ref_cells.source == 'file' and $ref_cells.file
13 list_of_cells=\$(cat $ref_cells.file | tr '\n' ',')
14 #end if
15 LANG=en_US.UTF-8 monocle3 topMarkers
16 --input-object-format cds3
17 #if $filter_fraction_expression
18 --filter-fraction-expression '$filter_fraction_expression'
19 #end if
20 #if $top_n_markers
21 --top-n-markers '$top_n_markers'
22 #end if
23 #if $plot_top_markers
24 --plot-top-markers top_markers.pdf
25 #end if
26 #if $save_full_markers
27 --save-full-markers full_markers.tsv
28 #end if
29 #if $ref_cells.source == 'file' and $ref_cells.file
30 --reference-cells \$list_of_cells
31 #end if
32 #if $ref_cells.source == 'number' and $ref_cells.number
33 --reference-cells '$ref_cells.number'
34 #end if
35 #if $marker_sig_test
36 --marker-sig-test
37 #end if
38 #if $genes_to_test_per_group
39 --genes-to-test-per-group '$genes_to_test_per_group'
40 #end if
41 #if $group_cells_by
42 --group-cells-by '$group_cells_by'
43 #end if
44 --cores \${GALAXY_SLOTS:-1}
45 --introspective
46
47 input.rds
48 output.tsv
49 ]]></command>
50 <inputs>
51 <param label="Input Object" name="input_object" type="data" format='rdata' help="Input file with monocle3 object cds3 in RDS"/>
52 <conditional name="ref_cells">
53 <param label="Reference cells source" name="source" type="select" argument="--reference-cells" help="(Optional) Set of cells to be considered as reference for marker significance test. Accelerates the marker significance test at some cost in sensitivity.">
54 <option value="file">File</option>
55 <option value="number">Number of cells</option>
56 </param>
57 <when value="file">
58 <param label="Reference cells file" name="file" optional="true" argument="--reference-cells" type="data" format='txt' help="File with cells to be used as reference cells."/>
59 </when>
60 <when value="number">
61 <param label="Number of reference cells" name="number" optional="true" argument="--reference-cells" type="integer" help="Number of cells to be used as reference cells."/>
62 </when>
63 </conditional>
64 <param label="Filter fraction for expression" optional='true' value="0.1" name="filter_fraction_expression" argument="--filter-fraction-expression" type="float" help="Filters the markers test result by this fraction of expression"/>
65 <param label="Top-n-markers" optional='true' value="5" name="top_n_markers" argument="--top-n-markers" type="integer" help="The number of top marker genes to report in plots and in top markers list"/>
66 <param label="Number of genes to test per group" optional='true' value="25" name="genes_to_test_per_group" argument="--genes-to-test-per-group" type="integer" help="how many genes of the top ranked specific genes by Jenson-Shannon, to do the more expensive regression test on"/>
67 <param label="Group cell by" optional='true' value='cluster' name="group_cells_by" argument="--group-cells-by" type="text" help="Cell groups, choose from 'cluster', 'partition', or any categorical variable in `colData(cds)`"/>
68 <param label="Use logistic regression to asses discriminatory power" value='false' name="marker_sig_test" argument="--marker-sig-test" type="boolean" checked='false' help="whether to assess the discriminative power of each marker through logistic regression. Can be slow, consider disabling to speed up top_markers()."/>
69 <param label="Save full markers" value='false' name="save_full_markers" argument="--save-full-markers" type="boolean" checked='false' help="whether to generate the full markers list as well."/>
70 <param label="Plot top markers" value='false' name="plot_top_markers" argument="--plot-top-markers" type="boolean" checked='true' help="whether to generate the top markers plot."/>
71 </inputs>
72
73 <outputs>
74 <data label="${tool.name} on ${on_string}: Top markers plot" name="top_markers_plot" format='pdf' from_work_dir='top_markers.pdf'>
75 <filter>plot_top_markers</filter>
76 </data>
77 <data label="${tool.name} on ${on_string}: Full markers" name="full_markers" from_work_dir="full_markers.tsv" format='tabular'>
78 <filter>save_full_markers</filter>
79 </data>
80 <data label="${tool.name} on ${on_string}: Top markers" name="top_markers_table" from_work_dir="output.tsv" format='tabular' />
81 </outputs>
82
83 <tests>
84 <test>
85 <param name="input_object_file" value="input.rds"/>
86 <param name="filter_fraction_expression" value="0.1"/>
87 <output name="top_markers_table" file="top_markers_table.tsv" ftype="tsv" compare="sim_size"/>
88 </test>
89 </tests>
90
91 <help><![CDATA[
92 ==========================================================
93 Monocle3 top markers genes
94 ==========================================================
95
96 Identify the genes most specifically expressed in groups of cells. See inline help for options.
97
98 @HELP@
99
100 @VERSION_HISTORY@
101 ]]></help>
102 <expand macro="citations"/>
103 </tool>