Mercurial > repos > ebi-gxa > monocle3_topmarkers

comparison monocle3-macros.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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-1:000000000000 0:bc2df96ef963
1 <macros>
2 <token name="@TOOL_VERSION@">0.1.4</token>
3 <token name="@PROFILE@">18.01</token>
4 <token name="@HELP@">More information can be found at https://cole-trapnell-lab.github.io/monocle3/ and https://github.com/ebi-gene-expression-group/monocle-scripts</token>
5 <token name="@VERSION_HISTORY@"><![CDATA[
6 **Version history**
7 0.1.5+galaxy0: Updated to monocle3-cli 0.0.8 to add top marker genes and fix container plots for plotCells (only those two modules upgraded).
8
9 0.1.4+galaxy0: Updated to monocle3-cli 0.0.7 to fix bug with column headers in tsv.
10
11 0.1.3+galaxy0: Updated to monocle3-cli 0.0.5 to fix bug with tsv inputs.
12
13 0.1.2+galaxy0: Initial version based on monocle3-cli 0.0.3 and monocle3 0.1.2
14 ]]></token>
15 <token name="@INPUT_OPTS@">
16 --input-object-format '${input_object_format}' '${input_object_file}'
17 </token>
18 <token name="@OUTPUT_OPTS@">
19 --output-object-format '${output_object_format}' output.RDS
20 #if $introspective
21 --introspective
22 #end if
23 </token>
24 <token name="@VERBOSE@">
25 #if $verbose
26 --verbose
27 #end if
28 </token>
29
30 <xml name="requirements">
31 <requirements>
32 <requirement type="package" version="0.0.7">monocle3-cli</requirement>
33 <yield/>
34 </requirements>
35 </xml>
36
37 <xml name="citations">
38 <citations>
39 <yield />
40 <citation type="doi">10.1038/nmeth.4402</citation>
41 <citation type="bibtex">
42 @misc{githubscanpy-scripts,
43 author = {Ni Huang, Krzysztof Polanski, EBI Gene Expression Team},
44 year = {2019},
45 title = {Monocle3-cli: command line interface for Monocle3},
46 publisher = {GitHub},
47 journal = {GitHub repository},
48 url = {https://github.com/ebi-gene-expression-group/monocle-scripts},
49 }</citation>
50 <citation type="doi">10.1101/2020.04.08.032698</citation>
51 </citations>
52 </xml>
53
54 <xml name="input_object_params">
55 <param name="input_object_file" argument="input-object-file" type="data" format="rdata" label="Input object in RDS format"/>
56 <param name="input_object_format" argument="--input-object-format" type="select" label="Format of input object">
57 <option value="cds3" selected="true">Monocle3 object in RDS</option>
58 </param>
59 </xml>
60
61 <xml name="output_object_params">
62 <param name="output_object_format" argument="--output-object-format" type="select" label="Format of output object">
63 <option value="cds3" selected="true">Monocle3 object in RDS</option>
64 </param>
65 <param name="introspective" argument="--introspective" type="boolean" checked="true" label="Print introspective information of output object"/>
66 </xml>
67
68 <xml name="verbose_flag">
69 <param name="verbose" argument="--verbose" type="boolean" checked="false" label="Emit verbose output"/>
70 </xml>
71 </macros>