Mercurial > repos > ebi-gxa > scanpy_run_fdg

comparison scanpy_macros2.xml @ 0:96af0059b974 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 08:23:52 -0400
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children 646e7e3044ca
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-1:000000000000 0:96af0059b974
1 <macros>
2 <token name="@TOOL_VERSION@">1.4.2</token>
3 <token name="@HELP@">More information can be found at https://scanpy.readthedocs.io</token>
4 <token name="@VERSION_HISTORY@"><![CDATA[
5 **Version history**
6
7 1.4.2+galaxy0: Update to scanpy-scripts 0.2.4 (requires scanpy >=1.4.2).
8
9 1.3.2+galaxy1: Normalise-data and filter-genes: Exposes ability to output 10x files.
10
11 1.3.2+galaxy0: Initial contribution. Ni Huang and Pablo Moreno, Expression Atlas team https://www.ebi.ac.uk/gxa/home at
12 EMBL-EBI https://www.ebi.ac.uk/ and Teichmann Lab at Wellcome Sanger Institute.
13 ]]></token>
14 <token name="@INPUT_OPTS@">
15 --input-format '${input_format}' input.h5
16 </token>
17 <token name="@OUTPUT_OPTS@">
18 --show-obj stdout --output-format '${output_format}' output.h5
19 </token>
20 <token name="@PLOT_OPTS@">
21 #if $fig_title
22 --title '${fig_title}'
23 #end if
24 --fig-size '${fig_size}'
25 --fig-dpi ${fig_dpi}
26 --fig-fontsize ${fig_fontsize}
27 ${fig_frame}
28 ./output.png
29 </token>
30 <token name="@EXPORT_MTX_OPTS@">${export_mtx}</token>
31
32 <xml name="requirements">
33 <requirements>
34 <requirement type="package" version="0.2.4.post4">scanpy-scripts</requirement>
35 <yield/>
36 </requirements>
37 </xml>
38
39 <xml name="citations">
40 <citations>
41 <yield />
42 <citation type="doi">10.1186/s13059-017-1382-0</citation>
43 <citation type="bibtex">
44 @misc{githubscanpy-scripts,
45 author = {Ni Huang, EBI Gene Expression Team},
46 year = {2018},
47 title = {Scanpy-scripts: command line interface for Scanpy},
48 publisher = {GitHub},
49 journal = {GitHub repository},
50 url = {https://github.com/ebi-gene-expression-group/scanpy-scripts},
51 }</citation>
52 </citations>
53 </xml>
54
55 <xml name="input_object_params">
56 <param name="input_obj_file" argument="input-object-file" type="data" format="h5" label="Input object in hdf5 format"/>
57 <param name="input_format" argument="--input-format" type="select" label="Format of input object">
58 <option value="anndata" selected="true">AnnData format hdf5</option>
59 <option value="loom">Loom format hdf5</option>
60 </param>
61 </xml>
62
63 <xml name="output_object_params">
64 <param name="output_format" argument="--output-format" type="select" label="Format of output object">
65 <option value="anndata" selected="true">AnnData format hdf5</option>
66 <option value="loom">Loom format hdf5</option>
67 </param>
68 </xml>
69
70 <xml name="output_plot_params">
71 <param name="fig_title" argument="--title" type="text" label="Figure title"/>
72 <param name="fig_size" argument="--fig-size" type="text" value="4,4" label="Figure size as 'width,height', e.g, '7,7'"/>
73 <param name="fig_dpi" argument="--fig-dpi" type="integer" min="1" value="80" label="Figure dpi"/>
74 <param name="fig_fontsize" argument="--fig-fontsize" type="integer" min="0" value="10" label="Figure font size"/>
75 <param name="fig_frame" type="boolean" truevalue="--frameon" falsevalue="--frameoff" checked="false"
76 label="Show plot frame"/>
77 </xml>
78
79 <xml name="export_mtx_params">
80 <param name="export_mtx" argument="--export-mtx" type="boolean" truevalue="--export-mtx ./" falsevalue="" checked="false" label="Save normalised data to 10x mtx format" help="If enabled, it will generate in addition to the main output in Loom or AnnData an export in 10x format of the normalised data."/>
81 </xml>
82
83 <xml name="export_mtx_outputs">
84 <data name="matrix_10x" format="txt" from_work_dir="matrix.mtx" label="${tool.name} on ${on_string}: 10x matrix">
85 <filter>export_mtx</filter>
86 </data>
87 <data name="genes_10x" format="tsv" from_work_dir="genes.tsv" label="${tool.name} on ${on_string}: 10x genes">
88 <filter>export_mtx</filter>
89 </data>
90 <data name="barcodes_10x" format="tsv" from_work_dir="barcodes.tsv" label="${tool.name} on ${on_string}: 10x barcodes">
91 <filter>export_mtx</filter>
92 </data>
93 </xml>
94 </macros>