Mercurial > repos > ebi-gxa > scanpy_multiplet_scrublet

comparison scanpy_macros2.xml @ 0:9f8381c5d808 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
author ebi-gxa
date Thu, 22 Jul 2021 20:57:12 +0000
parents
children 70cb0596ffef
comparison
equal deleted inserted replaced
-1:000000000000 0:9f8381c5d808
1 <macros>
2 <token name="@TOOL_VERSION@">1.8.1</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 1.8.1+galaxy0: Upate to scanpy-scripts 1.0.1 (running scanpy ==1.8.1), including Scrublet integration.
9
10 1.7.2+galaxy0: Upate to scanpy-scripts 0.3.3 (running scanpy ==1.7.2) to incorporate fix for object output from PAGA plotting, to allow PAGA init of FDG.
11
12 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
13 EMBL-EBI https://www.ebi.ac.uk/
14
15 1.4.3+galaxy10: Update to scanpy-scripts 0.2.10 (running scanpy ==1.4.3) to address bugfixes in run-pca.
16
17 1.4.3+galaxy10: Update to scanpy-scripts 0.2.9 (running scanpy ==1.4.3) to address bugfixes in find-variable-genes.
18
19 1.4.3+galaxy10: Use profile 18.01 for modules.
20
21 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.
22
23 1.4.3+galaxy0: Update to scanpy-scripts 0.2.5 (running scanpy ==1.4.3).
24
25 1.4.2+galaxy0: Update to scanpy-scripts 0.2.4 (requires scanpy >=1.4.2).
26
27 1.3.2+galaxy1: Normalise-data and filter-genes: Exposes ability to output 10x files.
28
29 1.3.2+galaxy0: Initial contribution. Ni Huang and Pablo Moreno, Expression Atlas team https://www.ebi.ac.uk/gxa/home at
30 EMBL-EBI https://www.ebi.ac.uk/ and Teichmann Lab at Wellcome Sanger Institute.
31 ]]></token>
32 <token name="@INPUT_OPTS@">
33 --input-format '${input_format}' input.h5
34 </token>
35 <token name="@SAVE_MATRIX_OPTS@">
36 #if $save_raw
37 --save-raw
38 #end if
39 #if $save_layer
40 --save-layer ${settings.save_layer}
41 #end if
42 </token>
43 <token name="@OUTPUT_OPTS@">
44 #if str($output_format).startswith('anndata')
45 --show-obj stdout --output-format anndata output.h5
46 #else
47 --show-obj stdout --output-format loom output.h5
48 #end if
49 </token>
50 <token name="@PLOT_OPTS@">
51 #if $fig_title
52 --title '${fig_title}'
53 #end if
54 --fig-size '${fig_size}'
55 --fig-dpi ${fig_dpi}
56 --fig-fontsize ${fig_fontsize}
57 ${fig_frame}
58 ./output.png
59 </token>
60 <token name="@EXPORT_MTX_OPTS@">${export_mtx}</token>
61
62 <xml name="requirements">
63 <requirements>
64 <requirement type="package" version="1.1.0">scanpy-scripts</requirement>
65 <yield/>
66 </requirements>
67 </xml>
68
69 <xml name="citations">
70 <citations>
71 <yield />
72 <citation type="doi">10.1186/s13059-017-1382-0</citation>
73 <citation type="bibtex">
74 @misc{githubscanpy-scripts,
75 author = {Ni Huang, EBI Gene Expression Team},
76 year = {2018},
77 title = {Scanpy-scripts: command line interface for Scanpy},
78 publisher = {GitHub},
79 journal = {GitHub repository},
80 url = {https://github.com/ebi-gene-expression-group/scanpy-scripts},
81 }</citation>
82 <citation type="doi">10.1101/2020.04.08.032698</citation>
83 <citation type="doi">10.1038/s41592-021-01102-w</citation>
84 </citations>
85 </xml>
86
87 <xml name="input_object_params">
88 <param name="input_obj_file" argument="input-object-file" type="data" format="h5,h5ad" label="Input object in AnnData/Loom format"/>
89 <param name="input_format" argument="--input-format" type="select" label="Format of input object">
90 <option value="anndata" selected="true">AnnData format hdf5</option>
91 <option value="loom">Loom format hdf5</option>
92 </param>
93 </xml>
94
95 <xml name="output_object_params">
96 <param name="output_format" argument="--output-format" type="select" label="Format of output object">
97 <option value="anndata_h5ad" selected="true">AnnData format</option>
98 <option value="anndata">AnnData format (h5 for older versions)</option>
99 <option value="loom">Loom format</option>
100 <option value="loom_legacy">Loom format (h5 for older versions)</option>
101 </param>
102 </xml>
103
104 <xml name="output_object_params_no_loom">
105 <param name="output_format" argument="--output-format" type="select" label="Format of output object">
106 <option value="anndata_h5ad" selected="true">AnnData format</option>
107 <option value="anndata">AnnData format (h5 for older versions)</option>
108 </param>
109 </xml>
110
111 <xml name="output_data_obj_no_loom" token_description="operation">
112 <data name="output_h5ad" format="h5ad" from_work_dir="output.h5" label="${tool.name} on ${on_string}: @DESCRIPTION@ AnnData">
113 <filter>output_format == 'anndata_h5ad'</filter>
114 </data>
115 <data name="output_h5" format="h5" from_work_dir="output.h5" label="${tool.name} on ${on_string}: @DESCRIPTION@ AnnData">
116 <filter>output_format == 'anndata'</filter>
117 </data>
118 </xml>
119
120 <xml name="output_data_obj" token_description="operation">
121 <data name="output_h5ad" format="h5ad" from_work_dir="output.h5" label="${tool.name} on ${on_string}: @DESCRIPTION@ AnnData">
122 <filter>output_format == 'anndata_h5ad'</filter>
123 </data>
124 <data name="output_h5" format="h5" from_work_dir="output.h5" label="${tool.name} on ${on_string}: @DESCRIPTION@ AnnData">
125 <filter>output_format == 'anndata'</filter>
126 </data>
127 <data name="output_loom_legacy" format="h5" from_work_dir="output.h5" label="${tool.name} on ${on_string}: @DESCRIPTION@ Loom">
128 <filter>output_format == 'loom_legacy'</filter>
129 </data>
130 <data name="output_loom" format="loom" from_work_dir="output.h5" label="${tool.name} on ${on_string}: @DESCRIPTION@ Loom">
131 <filter>output_format == 'loom'</filter>
132 </data>
133 </xml>
134
135 <xml name="save_matrix_params">
136 <param name="save_raw" argument="--save-raw" type="boolean" truevalue="yes" falsevalue="no" checked="false"
137 label="Save adata to adata.raw before processing?" />
138 <param name="save_layer" argument="--save-layer" type="text" optional="true"
139 label="Save adata.X to the specified layer before processing."/>
140 </xml>
141
142 <xml name="output_plot_params">
143 <param name="fig_title" argument="--title" type="text" label="Figure title"/>
144 <param name="fig_size" argument="--fig-size" type="text" value="4,4" label="Figure size as 'width,height', e.g, '7,7'"/>
145 <param name="fig_dpi" argument="--fig-dpi" type="integer" min="1" value="80" label="Figure dpi"/>
146 <param name="fig_fontsize" argument="--fig-fontsize" type="integer" min="0" value="10" label="Figure font size"/>
147 <param name="fig_frame" type="boolean" truevalue="--frameon" falsevalue="--frameoff" checked="false"
148 label="Show plot frame"/>
149 </xml>
150
151 <xml name="export_mtx_params">
152 <param name="export_mtx" argument="--export-mtx" type="boolean" truevalue="--export-mtx ./" falsevalue="" checked="false" label="Save to 10x mtx format" help="If enabled, it will generate in addition to the main output in Loom or AnnData an export in 10x format."/>
153 </xml>
154
155 <xml name="export_mtx_outputs">
156 <data name="matrix_10x" format="txt" from_work_dir="matrix.mtx" label="${tool.name} on ${on_string}: 10x matrix">
157 <filter>export_mtx</filter>
158 </data>
159 <data name="genes_10x" format="tsv" from_work_dir="genes.tsv" label="${tool.name} on ${on_string}: 10x genes">
160 <filter>export_mtx</filter>
161 </data>
162 <data name="barcodes_10x" format="tsv" from_work_dir="barcodes.tsv" label="${tool.name} on ${on_string}: 10x barcodes">
163 <filter>export_mtx</filter>
164 </data>
165 </xml>
166 </macros>