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comparison scanpy_macros2.xml @ 0:086d850271a2 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 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
author ebi-gxa
date Tue, 19 Nov 2019 13:00:14 -0500
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children 339d205356c6
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-1:000000000000 0:086d850271a2
1 <macros>
2 <token name="@TOOL_VERSION@">1.4.3</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 1.4.3+galaxy0: Update to scanpy-scripts 0.2.5 (running scanpy ==1.4.3).
8
9 1.4.2+galaxy0: Update to scanpy-scripts 0.2.4 (requires scanpy >=1.4.2).
10
11 1.3.2+galaxy1: Normalise-data and filter-genes: Exposes ability to output 10x files.
12
13 1.3.2+galaxy0: Initial contribution. Ni Huang and Pablo Moreno, Expression Atlas team https://www.ebi.ac.uk/gxa/home at
14 EMBL-EBI https://www.ebi.ac.uk/ and Teichmann Lab at Wellcome Sanger Institute.
15 ]]></token>
16 <token name="@INPUT_OPTS@">
17 --input-format '${input_format}' input.h5
18 </token>
19 <token name="@OUTPUT_OPTS@">
20 --show-obj stdout --output-format '${output_format}' output.h5
21 </token>
22 <token name="@PLOT_OPTS@">
23 #if $fig_title
24 --title '${fig_title}'
25 #end if
26 --fig-size '${fig_size}'
27 --fig-dpi ${fig_dpi}
28 --fig-fontsize ${fig_fontsize}
29 ${fig_frame}
30 ./output.png
31 </token>
32 <token name="@EXPORT_MTX_OPTS@">${export_mtx}</token>
33
34 <xml name="requirements">
35 <requirements>
36 <requirement type="package" version="0.2.5.post1">scanpy-scripts</requirement>
37 <yield/>
38 </requirements>
39 </xml>
40
41 <xml name="citations">
42 <citations>
43 <yield />
44 <citation type="doi">10.1186/s13059-017-1382-0</citation>
45 <citation type="bibtex">
46 @misc{githubscanpy-scripts,
47 author = {Ni Huang, EBI Gene Expression Team},
48 year = {2018},
49 title = {Scanpy-scripts: command line interface for Scanpy},
50 publisher = {GitHub},
51 journal = {GitHub repository},
52 url = {https://github.com/ebi-gene-expression-group/scanpy-scripts},
53 }</citation>
54 </citations>
55 </xml>
56
57 <xml name="input_object_params">
58 <param name="input_obj_file" argument="input-object-file" type="data" format="h5" label="Input object in hdf5 format"/>
59 <param name="input_format" argument="--input-format" type="select" label="Format of input object">
60 <option value="anndata" selected="true">AnnData format hdf5</option>
61 <option value="loom">Loom format hdf5</option>
62 </param>
63 </xml>
64
65 <xml name="output_object_params">
66 <param name="output_format" argument="--output-format" type="select" label="Format of output object">
67 <option value="anndata" selected="true">AnnData format hdf5</option>
68 <option value="loom">Loom format hdf5</option>
69 </param>
70 </xml>
71
72 <xml name="output_plot_params">
73 <param name="fig_title" argument="--title" type="text" label="Figure title"/>
74 <param name="fig_size" argument="--fig-size" type="text" value="4,4" label="Figure size as 'width,height', e.g, '7,7'"/>
75 <param name="fig_dpi" argument="--fig-dpi" type="integer" min="1" value="80" label="Figure dpi"/>
76 <param name="fig_fontsize" argument="--fig-fontsize" type="integer" min="0" value="10" label="Figure font size"/>
77 <param name="fig_frame" type="boolean" truevalue="--frameon" falsevalue="--frameoff" checked="false"
78 label="Show plot frame"/>
79 </xml>
80
81 <xml name="export_mtx_params">
82 <param name="export_mtx" argument="--export-mtx" type="boolean" truevalue="--export-mtx ./" falsevalue="" checked="false" label="Save 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."/>
83 </xml>
84
85 <xml name="export_mtx_outputs">
86 <data name="matrix_10x" format="txt" from_work_dir="matrix.mtx" label="${tool.name} on ${on_string}: 10x matrix">
87 <filter>export_mtx</filter>
88 </data>
89 <data name="genes_10x" format="tsv" from_work_dir="genes.tsv" label="${tool.name} on ${on_string}: 10x genes">
90 <filter>export_mtx</filter>
91 </data>
92 <data name="barcodes_10x" format="tsv" from_work_dir="barcodes.tsv" label="${tool.name} on ${on_string}: 10x barcodes">
93 <filter>export_mtx</filter>
94 </data>
95 </xml>
96 </macros>