Mercurial > repos > ebi-gxa > scanpy_integrate_combat

comparison scanpy_macros2.xml @ 0:2472523c0c50 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 62f47287c7e8449c59a1f1f454852ddc669b1b1e-dirty"
author ebi-gxa
date Mon, 07 Sep 2020 13:06:34 +0000
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children 27c74c83eae5
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-1:000000000000 0:2472523c0c50
1 <macros>
2 <token name="@TOOL_VERSION@">1.6.0</token>
3 <token name="@HELP@">More information can be found at https://scanpy.readthedocs.io</token>
4 <token name="@PROFILE@">18.01</token>
5 <token name="@VERSION_HISTORY@"><![CDATA[
6 **Version history**
7
8 1.6.0+galaxy0: Update to scanpy-scripts 0.2.13 (running scanpy ==1.6.0) to incorporate new options, code simplifications, and batch integration methods. Jonathan Manning, Expression Atlas team https://www.ebi.ac.uk/gxa/home at
9 EMBL-EBI https://www.ebi.ac.uk/
10
11 1.4.3+galaxy10: Update to scanpy-scripts 0.2.10 (running scanpy ==1.4.3) to address bugfixes in run-pca.
12
13 1.4.3+galaxy10: Update to scanpy-scripts 0.2.9 (running scanpy ==1.4.3) to address bugfixes in find-variable-genes.
14
15 1.4.3+galaxy10: Use profile 18.01 for modules.
16
17 1.4.3+galaxy6: Update to scanpy-scripts 0.2.8 (running scanpy ==1.4.3) and wider compatibility with other Galaxy modules. Bug fixes in filtering and plotting improvements.
18
19 1.4.3+galaxy0: Update to scanpy-scripts 0.2.5 (running scanpy ==1.4.3).
20
21 1.4.2+galaxy0: Update to scanpy-scripts 0.2.4 (requires scanpy >=1.4.2).
22
23 1.3.2+galaxy1: Normalise-data and filter-genes: Exposes ability to output 10x files.
24
25 1.3.2+galaxy0: Initial contribution. Ni Huang and Pablo Moreno, Expression Atlas team https://www.ebi.ac.uk/gxa/home at
26 EMBL-EBI https://www.ebi.ac.uk/ and Teichmann Lab at Wellcome Sanger Institute.
27 ]]></token>
28 <token name="@INPUT_OPTS@">
29 --input-format '${input_format}' input.h5
30 </token>
31 <token name="@OUTPUT_OPTS@">
32 #if str($output_format).startswith('anndata')
33 --show-obj stdout --output-format anndata output.h5
34 #else
35 --show-obj stdout --output-format loom output.h5
36 #end if
37 </token>
38 <token name="@PLOT_OPTS@">
39 #if $fig_title
40 --title '${fig_title}'
41 #end if
42 --fig-size '${fig_size}'
43 --fig-dpi ${fig_dpi}
44 --fig-fontsize ${fig_fontsize}
45 ${fig_frame}
46 ./output.png
47 </token>
48 <token name="@EXPORT_MTX_OPTS@">${export_mtx}</token>
49
50 <xml name="requirements">
51 <requirements>
52 <requirement type="package" version="0.3.0">scanpy-scripts</requirement>
53 <yield/>
54 </requirements>
55 </xml>
56
57 <xml name="citations">
58 <citations>
59 <yield />
60 <citation type="doi">10.1186/s13059-017-1382-0</citation>
61 <citation type="bibtex">
62 @misc{githubscanpy-scripts,
63 author = {Ni Huang, EBI Gene Expression Team},
64 year = {2018},
65 title = {Scanpy-scripts: command line interface for Scanpy},
66 publisher = {GitHub},
67 journal = {GitHub repository},
68 url = {https://github.com/ebi-gene-expression-group/scanpy-scripts},
69 }</citation>
70 <citation type="doi">10.1101/2020.04.08.032698</citation>
71 </citations>
72 </xml>
73
74 <xml name="input_object_params">
75 <param name="input_obj_file" argument="input-object-file" type="data" format="h5,h5ad" label="Input object in AnnData/Loom format"/>
76 <param name="input_format" argument="--input-format" type="select" label="Format of input object">
77 <option value="anndata" selected="true">AnnData format hdf5</option>
78 <option value="loom">Loom format hdf5</option>
79 </param>
80 </xml>
81
82 <xml name="output_object_params">
83 <param name="output_format" argument="--output-format" type="select" label="Format of output object">
84 <option value="anndata_h5ad" selected="true">AnnData format</option>
85 <option value="anndata">AnnData format (h5 for older versions)</option>
86 <option value="loom">Loom format</option>
87 <option value="loom_legacy">Loom format (h5 for older versions)</option>
88 </param>
89 </xml>
90
91 <xml name="output_object_params_no_loom">
92 <param name="output_format" argument="--output-format" type="select" label="Format of output object">
93 <option value="anndata_h5ad" selected="true">AnnData format</option>
94 <option value="anndata">AnnData format (h5 for older versions)</option>
95 </param>
96 </xml>
97
98 <xml name="output_data_obj_no_loom" token_description="operation">
99 <data name="output_h5ad" format="h5ad" from_work_dir="output.h5" label="${tool.name} on ${on_string}: @DESCRIPTION@ AnnData">
100 <filter>output_format == 'anndata_h5ad'</filter>
101 </data>
102 <data name="output_h5" format="h5" from_work_dir="output.h5" label="${tool.name} on ${on_string}: @DESCRIPTION@ AnnData">
103 <filter>output_format == 'anndata'</filter>
104 </data>
105 </xml>
106
107 <xml name="output_data_obj" token_description="operation">
108 <data name="output_h5ad" format="h5ad" from_work_dir="output.h5" label="${tool.name} on ${on_string}: @DESCRIPTION@ AnnData">
109 <filter>output_format == 'anndata_h5ad'</filter>
110 </data>
111 <data name="output_h5" format="h5" from_work_dir="output.h5" label="${tool.name} on ${on_string}: @DESCRIPTION@ AnnData">
112 <filter>output_format == 'anndata'</filter>
113 </data>
114 <data name="output_loom_legacy" format="h5" from_work_dir="output.h5" label="${tool.name} on ${on_string}: @DESCRIPTION@ Loom">
115 <filter>output_format == 'loom_legacy'</filter>
116 </data>
117 <data name="output_loom" format="loom" from_work_dir="output.h5" label="${tool.name} on ${on_string}: @DESCRIPTION@ Loom">
118 <filter>output_format == 'loom'</filter>
119 </data>
120 </xml>
121
122 <xml name="output_plot_params">
123 <param name="fig_title" argument="--title" type="text" label="Figure title"/>
124 <param name="fig_size" argument="--fig-size" type="text" value="4,4" label="Figure size as 'width,height', e.g, '7,7'"/>
125 <param name="fig_dpi" argument="--fig-dpi" type="integer" min="1" value="80" label="Figure dpi"/>
126 <param name="fig_fontsize" argument="--fig-fontsize" type="integer" min="0" value="10" label="Figure font size"/>
127 <param name="fig_frame" type="boolean" truevalue="--frameon" falsevalue="--frameoff" checked="false"
128 label="Show plot frame"/>
129 </xml>
130
131 <xml name="export_mtx_params">
132 <param name="export_mtx" argument="--export-mtx" type="boolean" truevalue="--export-mtx ./" falsevalue="" checked="false" label="Save to 10x mtx format" help="If enabled, it will generate in addition to the main output in Loom or AnnData an export in 10x format."/>
133 </xml>
134
135 <xml name="export_mtx_outputs">
136 <data name="matrix_10x" format="txt" from_work_dir="matrix.mtx" label="${tool.name} on ${on_string}: 10x matrix">
137 <filter>export_mtx</filter>
138 </data>
139 <data name="genes_10x" format="tsv" from_work_dir="genes.tsv" label="${tool.name} on ${on_string}: 10x genes">
140 <filter>export_mtx</filter>
141 </data>
142 <data name="barcodes_10x" format="tsv" from_work_dir="barcodes.tsv" label="${tool.name} on ${on_string}: 10x barcodes">
143 <filter>export_mtx</filter>
144 </data>
145 </xml>
146 </macros>