Mercurial > repos > ebi-gxa > ucsc_cell_browser

annotate cell-browser.xml @ 3:ad5179780e25 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 2ba483354c14ddfd0f7aa57c2ad1c9944e9c4bba"
author ebi-gxa
date Fri, 29 May 2020 07:09:58 -0400
parents 679dfd1dd63b
children 8da642e17794
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ad5179780e25 "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 2ba483354c14ddfd0f7aa57c2ad1c9944e9c4bba"
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1 <tool id="ucsc_cell_browser" name="UCSC Cell Browser" version="0.5.43+galaxy1" profile="18.01">
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2 <description>displays single-cell clusterized data in an interactive web application.</description>
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3 <requirements>
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679dfd1dd63b 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 7bf75360bdf687f987e706c3e48667931eaed0ce
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4 <requirement type="package" version="0.5.43">ucsc-cell-browser</requirement>
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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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5 </requirements>
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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>
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9 <command><![CDATA[
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10 #if $input_type.expression_source == "native-cell-browser":
1b43a2d812c9 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/ucsc-cell-browser/.shed.yml commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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ad5179780e25 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/ucsc-cell-browser/.shed.yml commit 2ba483354c14ddfd0f7aa57c2ad1c9944e9c4bba"
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12 echo "coords = [ {'file':'$tsneCoordinates', 'shortLabel':'t-SNE'} ]" > ./cellbrowser.conf;
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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;
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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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18 cbBuild -i cellbrowser.conf -o "$html_file.extra_files_path";
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ad5179780e25 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/ucsc-cell-browser/.shed.yml commit 2ba483354c14ddfd0f7aa57c2ad1c9944e9c4bba"
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ad5179780e25 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/ucsc-cell-browser/.shed.yml commit 2ba483354c14ddfd0f7aa57c2ad1c9944e9c4bba"
ebi-gxa
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20 ## "sample" is used as name, so no change needed.
ad5179780e25 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/ucsc-cell-browser/.shed.yml commit 2ba483354c14ddfd0f7aa57c2ad1c9944e9c4bba"
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21 cp '$__tool_directory__/redirect.html' '$html_file';
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23 #else if $input_type.expression_source == "cell-browser-tar":
1b43a2d812c9 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/ucsc-cell-browser/.shed.yml commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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25 tar -xf '$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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26 cbBuild -i cellbrowser.conf -o "$html_file.extra_files_path";
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ad5179780e25 "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 2ba483354c14ddfd0f7aa57c2ad1c9944e9c4bba"
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28 ## we need to adapt redirect to use the study name used in cellbrowser.conf
ad5179780e25 "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 2ba483354c14ddfd0f7aa57c2ad1c9944e9c4bba"
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29 study=\$(grep '^name=' cellbrowser.conf | awk -F'=' '{ print $2 }' | sed s/\"//g ) &&
ad5179780e25 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/ucsc-cell-browser/.shed.yml commit 2ba483354c14ddfd0f7aa57c2ad1c9944e9c4bba"
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30 echo "Study to replace: "\$study &&
ad5179780e25 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/ucsc-cell-browser/.shed.yml commit 2ba483354c14ddfd0f7aa57c2ad1c9944e9c4bba"
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31 sed "s/ds=sample/ds=\$study/" '$__tool_directory__/redirect.html' > '$html_file';
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33 #else if $input_type.expression_source == "scanpy":
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34
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35 ## We could add a condition here were, if cluster_field is provided
ad5179780e25 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/ucsc-cell-browser/.shed.yml commit 2ba483354c14ddfd0f7aa57c2ad1c9944e9c4bba"
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36 ## then we rename it inside with an AnnData relying script to read 'louvain' to please UCSC CellBrowser
ad5179780e25 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/ucsc-cell-browser/.shed.yml commit 2ba483354c14ddfd0f7aa57c2ad1c9944e9c4bba"
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37
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38 ln -s '$input_anndata_file' scanpy_ann_data.h5ad;
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ad5179780e25 "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 2ba483354c14ddfd0f7aa57c2ad1c9944e9c4bba"
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39 cbImportScanpy -i scanpy_ann_data.h5ad
ad5179780e25 "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 2ba483354c14ddfd0f7aa57c2ad1c9944e9c4bba"
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ad5179780e25 "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 2ba483354c14ddfd0f7aa57c2ad1c9944e9c4bba"
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41 #if $input_type.marker_field:
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42 --markerField '${input_type.marker_field}'
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43 #end if
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ad5179780e25 "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 2ba483354c14ddfd0f7aa57c2ad1c9944e9c4bba"
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45 -o outdir -n sample --htmlDir '$html_file.extra_files_path';
ad5179780e25 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/ucsc-cell-browser/.shed.yml commit 2ba483354c14ddfd0f7aa57c2ad1c9944e9c4bba"
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46 cp '$__tool_directory__/redirect.html' '$html_file';
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48 #end if
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49 ]]></command>
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50 <inputs>
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51 <conditional name="input_type">
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52 <param type="select" name="expression_source" label="Choose the format of the expression data" help="Use compressed txt, Scanpy or Seurat objects">
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53 <option value="native-cell-browser" selected="true">CellBrowser tar.gz expression matrix</option>
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54 <option value="scanpy">Scanpy AnnData HDF5 serialized object</option>
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55 <option value="cell-browser-tar">Tar file with CellBrowser files to execute cbBuild</option>
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56 </param>
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57 <when value="native-cell-browser">
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58 <param type="data" name="expressionMatrix" label="Expression matrix" help="Tabular expression matrix (see https://github.com/maximilianh/cellBrowser/tree/master/sampleData)" format="tabular"/>
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59 <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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60 <param type="data" name="tsneCoordinates" label="tSNE coordinates" help="Tabular file with tSNE coordinates for each cell." format="tabular"/>
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61 </when>
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62 <when value="cell-browser-tar">
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63 <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"/>
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64 </when>
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65 <when value="scanpy">
3
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66 <param name="input_anndata_file" type="data" format="h5,h5ad" label="Input object in AnnData hdf5 format" help="Scanpy serialized output is by default produced as an AnnData hdf5 file."/>
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67 <param name="marker_field" argument="--markerField" type="text" value="rank_genes_groups" label="Marker genes field" help="Scanpy marker genes field to use, optional, if not set 'rank_genes_groups' will be used."/>
0
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68 </when>
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69 </conditional>
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70 </inputs>
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71 <outputs>
3
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72 <data format="html" name="html_file" label="${tool.name} on ${on_string}: Interactive Viewer"/>
0
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73 </outputs>
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74
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75 <tests>
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76 <test>
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77 <param name="input_anndata_file" ftype="data" value="anndata.h5"/>
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78 <output name="html_file" ftype="data" value="cellbrowser.html" compare="sim_size"/>
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79 </test>
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80 </tests>
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81
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82 <help><![CDATA[
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83 UCSC Single Cell Browser
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84 ========================
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85
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86 Funded by the California Institute of Regenerative Medicine and the Chan-Zuckerberg
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87 Initiative https://www.chanzuckerberg.com/.
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88
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89 The UCSC Cell Browser is a viewer for single cell data. You can click on and hover
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90 over cells to get meta information, search for genes to color on and click clusters
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91 to show cluster-specific marker genes, which in turn are clickable again.
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92
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93 For a demo of the browser, see http://cells.ucsc.edu
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94
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95 Usage
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96 -----
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97
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98 After choosing the inputs and executing the tool, once the history item becomes
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99 green, press the View data (eye icon) button, which will open the generated UCSC Cell Browser
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100 interactive site. Press the white on blue "Open Dataset" button.
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101
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102 Troubleshooting
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103 ---------------
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104
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105 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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106 with the text "Choose cell...". If that is the case, close that panel (click on the cross)
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107 and then choose File -> Open Dataset... and then press the Open Dataset white button.
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108
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109 Version history
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110 ---------------
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111
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112 0.4.3+galaxy0: Initial contribution. Pablo Moreno, Expression Atlas team https://www.ebi.ac.uk/gxa/home at
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113 EMBL-EBI https://www.ebi.ac.uk/.
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114
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115 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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116 EMBL-EBI https://www.ebi.ac.uk/.
1
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117
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118 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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119 EMBL-EBI https://www.ebi.ac.uk/.
2
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120
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121 0.5.38+galaxy0: Update UCSC CellBrowser version to 0.5.43. Fixes bugs and improves usage of gene symbols in AnnData objects. Pablo Moreno, Expression Atlas team https://www.ebi.ac.uk/gxa/home at
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122 EMBL-EBI https://www.ebi.ac.uk/.
0
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123 ]]></help>
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124 <citations>
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125 <citation type="bibtex">
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126 @misc{ucsc-cell-browser-gitrepo,
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127 author = {Maximilian Haeussler and collaborators},
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128 year = {2018},
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129 title = {UCSC Single Cell Browser: Python pipeline and Javascript scatter plot library for single-cell datasets},
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130 publisher = {GitHub},
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131 journal = {GitHub repository},
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132 url = {https://github.com/maximilianh/cellBrowser},
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133 }
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134 </citation>
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ad5179780e25 "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 2ba483354c14ddfd0f7aa57c2ad1c9944e9c4bba"
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135 <citation type="doi">10.1101/2020.04.08.032698</citation>
0
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136 </citations>
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137 </tool>