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comparison scanpy_macros.xml @ 26:be019b069e31 draft default tip

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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 ee197a80b2d591c393e1662854bc119b2ecab11e-dirty
author ebi-gxa
date Tue, 27 Feb 2024 16:43:40 +0000
parents cef0ddd01875
children
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25:cef0ddd01875 26:be019b069e31
1 <macros>
2 <token name="@TOOL_VERSION@">1.3.2</token>
3 <token name="@HELP@">More information can be found at https://scanpy.readthedocs.io</token>
4 <token name="@PLOT_OPTS@">
5 #if $do_plotting.plot
6 -P output.png
7 --projectio $do_plotting.projection
8 --components $do_plotting.components
9 #if $do_plotting.color_by
10 --color-by $do_plotting.color_by
11 #end if
12 #if $do_plotting.groups
13 --group $do_plotting.groups
14 #end if
15 #if $do_plotting.use_raw
16 --use-raw
17 #end if
18 #if $do_plotting.palette
19 --palette $do_plotting.palette
20 #end if
21 #if $do_plotting.edges
22 --edges
23 #end if
24 #if $do_plotting.arrows
25 --arrows
26 #end if
27 #if not $do_plotting.sort_order
28 --no-sort-order
29 #end if
30 #if $do_plotting.frameoff
31 --frameoff
32 #end if
33 #end if
34 </token>
35 <xml name="requirements">
36 <requirements>
37 <requirement type="package" version="0.0.5">scanpy-scripts</requirement>
38 <yield/>
39 </requirements>
40 </xml>
41 <token name="@EXPORT_MTX_OPTS@">
42 ${export_mtx}
43 </token>
44 <token name="@VERSION_HISTORY@"><![CDATA[
45 **Version history**
46
47 1.3.2+galaxy1: Normalise-data and filter-genes: Exposes ability to output 10x files.
48
49 1.3.2+galaxy0: Initial contribution. Ni Huang and Pablo Moreno, Expression Atlas team https://www.ebi.ac.uk/gxa/home at
50 EMBL-EBI https://www.ebi.ac.uk/ and Teichmann Lab at Wellcome Sanger Institute.
51 ]]></token>
52 <xml name="citations">
53 <citations>
54 <citation type="doi">10.1186/s13059-017-1382-0</citation>
55 <citation type="bibtex">
56 @misc{githubscanpy-scripts,
57 author = {Ni Huang, EBI Gene Expression Team},
58 year = {2018},
59 title = {Scanpy-scripts: command line interface for Scanpy},
60 publisher = {GitHub},
61 journal = {GitHub repository},
62 url = {https://github.com/ebi-gene-expression-group/scanpy-scripts},
63 }</citation>
64 <yield />
65 </citations>
66 </xml>
67 <xml name="input_object_params">
68 <param name="input_obj_file" argument="--input-object-file" type="data" format="h5" label="Input object in hdf5 format"/>
69 <param name="input_format" argument="--input-format" type="select" label="Format of input object">
70 <option value="anndata" selected="true">AnnData format hdf5</option>
71 <option value="loom">Loom format hdf5, current support is incomplete</option>
72 </param>
73 </xml>
74 <xml name="output_object_params">
75 <param name="output_format" argument="--output-format" type="select" label="Format of output object">
76 <option value="anndata" selected="true">AnnData format hdf5</option>
77 <option value="loom">Loom format hdf5, current support is defective</option>
78 </param>
79 </xml>
80 <xml name="output_plot_params">
81 <param name="color_by" argument="--color-by" type="text" value="n_genes" label="Color by attributes, comma separated strings"/>
82 <param name="groups" argument="--groups" type="text" optional="ture" label="Restrict plotting to named groups, comma separated strings"/>
83 <param name="projection" argument="--projection" type="select" label="Plot projection">
84 <option value="2d" selected="true">2D</option>
85 <option value="3d">3D</option>
86 </param>
87 <param name="components" argument="--components" type="text" value="1,2" label="Components to plot, comma separated integers"/>
88 <param name="palette" argument="--palette" type="text" optional="true" label="Palette"/>
89 <param name="use_raw" argument="--use-raw" type="boolean" checked="false" label="Use raw attributes if present"/>
90 <param name="edges" argument="--edges" type="boolean" checked="false" label="Show edges"/>
91 <param name="arrows" argument="--arrows" type="boolean" checked="false" label="Show arrows"/>
92 <param name="sort_order" argument="--no-sort-order" type="boolean" checked="true" label="Element with high color-by value plot on top"/>
93 <param name="frameoff" argument="--frameoff" type="boolean" checked="false" label="Omit frame"/>
94 </xml>
95 <xml name="export_mtx_params">
96 <param name="export_mtx" argument="--export-mtx" type="boolean" truevalue="--export-mtx ./" falsevalue="" checked="false" label="Save normalised data to 10x 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."/>
97 </xml>
98 <xml name="export_mtx_outputs">
99 <data name="matrix_10x" format="txt" from_work_dir="matrix.mtx" label="${tool.name} on ${on_string}: 10x matrix">
100 <filter>export_mtx</filter>
101 </data>
102 <data name="genes_10x" format="tsv" from_work_dir="genes.tsv" label="${tool.name} on ${on_string}: 10x genes">
103 <filter>export_mtx</filter>
104 </data>
105 <data name="barcodes_10x" format="tsv" from_work_dir="barcodes.tsv" label="${tool.name} on ${on_string}: 10x barcodes">
106 <filter>export_mtx</filter>
107 </data>
108 </xml>
109 </macros>