Mercurial > repos > ebi-gxa > monocle3_ordercells

comparison monocle3-macros.xml @ 0:5520da33a868 draft

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"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
author ebi-gxa
date Mon, 16 Sep 2019 09:52:31 -0400
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children e17c3123cdb5
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-1:000000000000 0:5520da33a868
1 <macros>
2 <token name="@TOOL_VERSION@">0.1.2</token>
3 <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>
4 <token name="@VERSION_HISTORY@"><![CDATA[
5 **Version history**
6
7 0.1.2+galaxy0: Initial version based on monocle3-cli 0.0.3 and monocle3 0.1.2
8 ]]></token>
9 <token name="@INPUT_OPTS@">
10 --input-object-format '${input_object_format}' '${input_object_file}'
11 </token>
12 <token name="@OUTPUT_OPTS@">
13 --output-object-format '${output_object_format}' output.RDS
14 #if $introspective
15 --introspective
16 #end if
17 </token>
18 <token name="@VERBOSE@">
19 #if $verbose
20 --verbose
21 #end if
22 </token>
23
24 <xml name="requirements">
25 <requirements>
26 <requirement type="package" version="0.0.3">monocle3-cli</requirement>
27 <yield/>
28 </requirements>
29 </xml>
30
31 <xml name="citations">
32 <citations>
33 <yield />
34 <citation type="doi">10.1038/nmeth.4402</citation>
35 <citation type="bibtex">
36 @misc{githubscanpy-scripts,
37 author = {Ni Huang, Krzysztof Polanski, EBI Gene Expression Team},
38 year = {2019},
39 title = {Monocle3-cli: command line interface for Monocle3},
40 publisher = {GitHub},
41 journal = {GitHub repository},
42 url = {https://github.com/ebi-gene-expression-group/monocle-scripts},
43 }</citation>
44 </citations>
45 </xml>
46
47 <xml name="input_object_params">
48 <param name="input_object_file" argument="input-object-file" type="data" format="rdata" label="Input object in RDS format"/>
49 <param name="input_object_format" argument="--input-object-format" type="select" label="Format of input object">
50 <option value="cds3" selected="true">Monocle3 object in RDS</option>
51 </param>
52 </xml>
53
54 <xml name="output_object_params">
55 <param name="output_object_format" argument="--output-object-format" type="select" label="Format of output object">
56 <option value="cds3" selected="true">Monocle3 object in RDS</option>
57 </param>
58 <param name="introspective" argument="--introspective" type="boolean" checked="true" label="Print introspective information of output object"/>
59 </xml>
60
61 <xml name="verbose_flag">
62 <param name="verbose" argument="--verbose" type="boolean" checked="false" label="Emit verbose output"/>
63 </xml>
64 </macros>