Mercurial > repos > ebi-gxa > ucsc_cell_browser

comparison cell-browser.xml @ 0:1b43a2d812c9 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/ucsc-cell-browser/.shed.yml commit 9bf9a6e46a330890be932f60d1d996dd166426c4
author ebi-gxa
date Wed, 03 Apr 2019 11:56:43 -0400
parents
children 674777a022e4
comparison
equal deleted inserted replaced
-1:000000000000 0:1b43a2d812c9
1 <tool id="ucsc_cell_browser" name="UCSC Cell Browser" version="0.4.38+galaxy0">
2 <description>displays single-cell clusterized data in an interactive web application.</description>
3 <requirements>
4 <requirement type="package" version="0.4.38">ucsc-cell-browser</requirement>
5 </requirements>
6 <stdio>
7 <exit_code range="1:" />
8 </stdio>
9 <command><![CDATA[
10 #if $input_type.expression_source == "native-cell-browser":
11
12 echo "coords = [ {'file':'$tsneCoordinates', 'shortLabel':'t-SNE on WGCNA'} ]" > ./cellbrowser.conf;
13 echo "meta = '$cellMetadata'" >> ./cellbrowser.conf;
14 echo "name = 'sample'" >> ./cellbrowser.conf;
15 echo "exprMatrix = '$expressionMatrix'" >> ./cellbrowser.conf;
16 echo "geneIdType = 'symbol'" >> ./cellbrowser.conf;
17
18 cbBuild -i cellbrowser.conf -o "$html_file.extra_files_path";
19 mv "$html_file.extra_files_path"/index.html "$html_file";
20
21 #else if $input_type.expression_source == "cell-browser-tar":
22
23 tar -xf '$tarred_sources';
24 cbBuild -i cellbrowser.conf -o "$html_file.extra_files_path";
25 mv "$html_file.extra_files_path"/index.html "$html_file";
26
27 #else if $input_type.expression_source == "scanpy":
28
29 ln -s '$input_anndata_file' scanpy_ann_data.h5ad;
30 cbImportScanpy -i scanpy_ann_data.h5ad -o outdir -n sample --htmlDir "$html_file.extra_files_path";
31 mv "$html_file.extra_files_path"/index.html "$html_file";
32
33 #end if
34 ]]></command>
35 <inputs>
36 <conditional name="input_type">
37 <param type="select" name="expression_source" label="Choose the format of the expression data" help="Use compressed txt, Scanpy or Seurat objects">
38 <option value="native-cell-browser" selected="true">CellBrowser tar.gz expression matrix</option>
39 <option value="scanpy">Scanpy AnnData HDF5 serialized object</option>
40 <option value="cell-browser-tar">Tar file with CellBrowser files to execute cbBuild</option>
41 </param>
42 <when value="native-cell-browser">
43 <param type="data" name="expressionMatrix" label="Expression matrix" help="Tabular expression matrix (see https://github.com/maximilianh/cellBrowser/tree/master/sampleData)" format="tabular"/>
44 <param type="data" name="cellMetadata" label="Cell metadata" help="Tabular file with metadata fields (columns) for each cell (rows)." format="tabular"/>
45 <param type="data" name="tsneCoordinates" label="tSNE coordinates" help="Tabular file with tSNE coordinates for each cell." format="tabular"/>
46 </when>
47 <when value="cell-browser-tar">
48 <param name="tarred_sources" type="data" format="tar" label="CellBrowser source files tarred" help="Tar containing CellBrowser config, tsne, umap and other source files for running cbBuild"/>
49 </when>
50 <when value="scanpy">
51 <param name="input_anndata_file" type="data" format="h5" label="Input object in AnnData hdf5 format" help="Scanpy serialized output is by default produced as an AnnData hdf5 file."/>
52 </when>
53 </conditional>
54 </inputs>
55 <outputs>
56 <data format="html" name="html_file" label="Interactive UCSC Cell Browser"/>
57 </outputs>
58
59 <tests>
60 <test>
61 <param name="input_anndata_file" ftype="data" value="anndata.h5"/>
62 <output name="html_file" ftype="data" value="cellbrowser.html" compare="sim_size"/>
63 </test>
64 </tests>
65
66 <help><![CDATA[
67 UCSC Single Cell Browser
68 ========================
69
70 Funded by the California Institute of Regenerative Medicine and the Chan-Zuckerberg
71 Initiative https://www.chanzuckerberg.com/.
72
73 The UCSC Cell Browser is a viewer for single cell data. You can click on and hover
74 over cells to get meta information, search for genes to color on and click clusters
75 to show cluster-specific marker genes, which in turn are clickable again.
76
77 For a demo of the browser, see http://cells.ucsc.edu
78
79 Usage
80 -----
81
82 After choosing the inputs and executing the tool, once the history item becomes
83 green, press the View data (eye icon) button, which will open the generated UCSC Cell Browser
84 interactive site. Press the white on blue "Open Dataset" button.
85
86 Troubleshooting
87 ---------------
88
89 Depending on the window size when pressing the "View data" button, you might see a black canvas and a diminished panel to the upper left
90 with the text "Choose cell...". If that is the case, close that panel (click on the cross)
91 and then choose File -> Open Dataset... and then press the Open Dataset white button.
92
93 Version history
94 ---------------
95
96 0.4.3+galaxy0: Initial contribution. Pablo Moreno, Expression Atlas team https://www.ebi.ac.uk/gxa/home at
97 EMBL-EBI https://www.ebi.ac.uk/.
98
99 0.4.38+galaxy0: Supports Seurat (through a converter) and Scanpy input. Pablo Moreno, Expression Atlas team https://www.ebi.ac.uk/gxa/home at
100 EMBL-EBI https://www.ebi.ac.uk/.
101 ]]></help>
102 <citations>
103 <citation type="bibtex">
104 @misc{ucsc-cell-browser-gitrepo,
105 author = {Maximilian Haeussler and collaborators},
106 year = {2018},
107 title = {UCSC Single Cell Browser: Python pipeline and Javascript scatter plot library for single-cell datasets},
108 publisher = {GitHub},
109 journal = {GitHub repository},
110 url = {https://github.com/maximilianh/cellBrowser},
111 }
112 </citation>
113 </citations>
114 </tool>