Mercurial > repos > ebi-gxa > ucsc_cell_browser

annotate cell-browser.xml @ 1:674777a022e4 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/ucsc-cell-browser/.shed.yml commit 40504509141d54e959919111316a5196faf12bf7
author ebi-gxa
date Wed, 05 Jun 2019 11:15:38 -0400
parents 1b43a2d812c9
children 679dfd1dd63b
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674777a022e4 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 40504509141d54e959919111316a5196faf12bf7
ebi-gxa
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1 <tool id="ucsc_cell_browser" name="UCSC Cell Browser" version="0.5.21+galaxy0">
0
1b43a2d812c9 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
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2 <description>displays single-cell clusterized data in an interactive web application.</description>
1b43a2d812c9 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
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3 <requirements>
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674777a022e4 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 40504509141d54e959919111316a5196faf12bf7
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4 <requirement type="package" version="0.5.21">ucsc-cell-browser</requirement>
0
1b43a2d812c9 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
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5 </requirements>
1b43a2d812c9 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
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6 <stdio>
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7 <exit_code range="1:" />
1b43a2d812c9 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
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8 </stdio>
1b43a2d812c9 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
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9 <command><![CDATA[
1b43a2d812c9 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
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10 #if $input_type.expression_source == "native-cell-browser":
1b43a2d812c9 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/ucsc-cell-browser/.shed.yml commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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1b43a2d812c9 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/ucsc-cell-browser/.shed.yml commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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12 echo "coords = [ {'file':'$tsneCoordinates', 'shortLabel':'t-SNE on WGCNA'} ]" > ./cellbrowser.conf;
1b43a2d812c9 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
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13 echo "meta = '$cellMetadata'" >> ./cellbrowser.conf;
1b43a2d812c9 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/ucsc-cell-browser/.shed.yml commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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14 echo "name = 'sample'" >> ./cellbrowser.conf;
1b43a2d812c9 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/ucsc-cell-browser/.shed.yml commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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15 echo "exprMatrix = '$expressionMatrix'" >> ./cellbrowser.conf;
1b43a2d812c9 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
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16 echo "geneIdType = 'symbol'" >> ./cellbrowser.conf;
1b43a2d812c9 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
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1b43a2d812c9 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
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18 cbBuild -i cellbrowser.conf -o "$html_file.extra_files_path";
1b43a2d812c9 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/ucsc-cell-browser/.shed.yml commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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19 mv "$html_file.extra_files_path"/index.html "$html_file";
1b43a2d812c9 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
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21 #else if $input_type.expression_source == "cell-browser-tar":
1b43a2d812c9 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/ucsc-cell-browser/.shed.yml commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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22
1b43a2d812c9 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/ucsc-cell-browser/.shed.yml commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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23 tar -xf '$tarred_sources';
1b43a2d812c9 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
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24 cbBuild -i cellbrowser.conf -o "$html_file.extra_files_path";
1b43a2d812c9 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/ucsc-cell-browser/.shed.yml commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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25 mv "$html_file.extra_files_path"/index.html "$html_file";
1b43a2d812c9 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
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27 #else if $input_type.expression_source == "scanpy":
1b43a2d812c9 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/ucsc-cell-browser/.shed.yml commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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28
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29 ln -s '$input_anndata_file' scanpy_ann_data.h5ad;
1b43a2d812c9 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
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30 cbImportScanpy -i scanpy_ann_data.h5ad -o outdir -n sample --htmlDir "$html_file.extra_files_path";
1b43a2d812c9 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/ucsc-cell-browser/.shed.yml commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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31 mv "$html_file.extra_files_path"/index.html "$html_file";
1b43a2d812c9 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
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32
1b43a2d812c9 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
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33 #end if
1b43a2d812c9 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
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34 ]]></command>
1b43a2d812c9 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
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35 <inputs>
1b43a2d812c9 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
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36 <conditional name="input_type">
1b43a2d812c9 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
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37 <param type="select" name="expression_source" label="Choose the format of the expression data" help="Use compressed txt, Scanpy or Seurat objects">
1b43a2d812c9 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
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38 <option value="native-cell-browser" selected="true">CellBrowser tar.gz expression matrix</option>
1b43a2d812c9 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
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39 <option value="scanpy">Scanpy AnnData HDF5 serialized object</option>
1b43a2d812c9 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
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40 <option value="cell-browser-tar">Tar file with CellBrowser files to execute cbBuild</option>
1b43a2d812c9 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
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41 </param>
1b43a2d812c9 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
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42 <when value="native-cell-browser">
1b43a2d812c9 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
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43 <param type="data" name="expressionMatrix" label="Expression matrix" help="Tabular expression matrix (see https://github.com/maximilianh/cellBrowser/tree/master/sampleData)" format="tabular"/>
1b43a2d812c9 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
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44 <param type="data" name="cellMetadata" label="Cell metadata" help="Tabular file with metadata fields (columns) for each cell (rows)." format="tabular"/>
1b43a2d812c9 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
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45 <param type="data" name="tsneCoordinates" label="tSNE coordinates" help="Tabular file with tSNE coordinates for each cell." format="tabular"/>
1b43a2d812c9 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
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46 </when>
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47 <when value="cell-browser-tar">
1b43a2d812c9 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
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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"/>
1b43a2d812c9 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
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49 </when>
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50 <when value="scanpy">
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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."/>
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52 </when>
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53 </conditional>
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54 </inputs>
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55 <outputs>
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56 <data format="html" name="html_file" label="Interactive UCSC Cell Browser"/>
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57 </outputs>
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58
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59 <tests>
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60 <test>
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61 <param name="input_anndata_file" ftype="data" value="anndata.h5"/>
1b43a2d812c9 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
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62 <output name="html_file" ftype="data" value="cellbrowser.html" compare="sim_size"/>
1b43a2d812c9 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
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63 </test>
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64 </tests>
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65
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66 <help><![CDATA[
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67 UCSC Single Cell Browser
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68 ========================
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69
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70 Funded by the California Institute of Regenerative Medicine and the Chan-Zuckerberg
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71 Initiative https://www.chanzuckerberg.com/.
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72
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73 The UCSC Cell Browser is a viewer for single cell data. You can click on and hover
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74 over cells to get meta information, search for genes to color on and click clusters
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75 to show cluster-specific marker genes, which in turn are clickable again.
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76
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77 For a demo of the browser, see http://cells.ucsc.edu
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78
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79 Usage
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80 -----
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81
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82 After choosing the inputs and executing the tool, once the history item becomes
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83 green, press the View data (eye icon) button, which will open the generated UCSC Cell Browser
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84 interactive site. Press the white on blue "Open Dataset" button.
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85
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86 Troubleshooting
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87 ---------------
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88
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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
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90 with the text "Choose cell...". If that is the case, close that panel (click on the cross)
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91 and then choose File -> Open Dataset... and then press the Open Dataset white button.
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92
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93 Version history
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94 ---------------
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95
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96 0.4.3+galaxy0: Initial contribution. Pablo Moreno, Expression Atlas team https://www.ebi.ac.uk/gxa/home at
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97 EMBL-EBI https://www.ebi.ac.uk/.
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98
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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
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100 EMBL-EBI https://www.ebi.ac.uk/.
1
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101
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102 0.5.21+galaxy0: Update UCSC CellBrowser version to 0.5.21. Pablo Moreno, Expression Atlas team https://www.ebi.ac.uk/gxa/home at
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103 EMBL-EBI https://www.ebi.ac.uk/.
0
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104 ]]></help>
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105 <citations>
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106 <citation type="bibtex">
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107 @misc{ucsc-cell-browser-gitrepo,
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108 author = {Maximilian Haeussler and collaborators},
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109 year = {2018},
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110 title = {UCSC Single Cell Browser: Python pipeline and Javascript scatter plot library for single-cell datasets},
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111 publisher = {GitHub},
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112 journal = {GitHub repository},
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113 url = {https://github.com/maximilianh/cellBrowser},
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114 }
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115 </citation>
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116 </citations>
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117 </tool>