Mercurial > repos > ebi-gxa > ucsc_cell_browser

annotate cell-browser.xml @ 6:97483e5ec21e draft default tip

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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 30c232088d42557d13359dfa26f9c7ce5edfc444
author ebi-gxa
date Sat, 15 Jul 2023 09:25:00 +0000
parents 544d44faa8bf
children
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rev   line source
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97483e5ec21e 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 30c232088d42557d13359dfa26f9c7ce5edfc444
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1 <tool id="ucsc_cell_browser" name="UCSC Cell Browser" version="1.0.0+galaxy1" profile="18.01">
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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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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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4 <requirement type="package" version="1.0.0">ucsc-cell-browser</requirement>
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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:" />
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97483e5ec21e 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 30c232088d42557d13359dfa26f9c7ce5edfc444
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8 <regex source="both" match="Killed" level="fatal_oom" description="Killed, most likely due to OOM" />
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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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9 </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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10 <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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11 #if $input_type.expression_source == "native-cell-browser":
1b43a2d812c9 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/ucsc-cell-browser/.shed.yml commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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12
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13 echo "coords = [ {'file':'$tsneCoordinates', 'shortLabel':'t-SNE'} ]" > ./cellbrowser.conf;
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14 echo "meta = '$cellMetadata'" >> ./cellbrowser.conf;
1b43a2d812c9 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/ucsc-cell-browser/.shed.yml commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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15 echo "name = 'sample'" >> ./cellbrowser.conf;
1b43a2d812c9 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/ucsc-cell-browser/.shed.yml commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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16 echo "exprMatrix = '$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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17 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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19 cbBuild -i cellbrowser.conf -o "$html_file.extra_files_path";
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21 ## "sample" is used as name, so no change needed.
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544d44faa8bf "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/ucsc-cell-browser/.shed.yml commit a0e5240b76fcf613ebe0a18b99ac29cdc95e073f"
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22 # cp '$__tool_directory__/redirect.html' '$html_file';
544d44faa8bf "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/ucsc-cell-browser/.shed.yml commit a0e5240b76fcf613ebe0a18b99ac29cdc95e073f"
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23 mv '$redirect_html' '$html_file';
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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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25 #else if $input_type.expression_source == "cell-browser-tar":
1b43a2d812c9 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/ucsc-cell-browser/.shed.yml commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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27 tar -xf '$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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28 cbBuild -i cellbrowser.conf -o "$html_file.extra_files_path";
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30 ## we need to adapt redirect to use the study name used in cellbrowser.conf
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31 study=\$(grep '^name=' cellbrowser.conf | awk -F'=' '{ print $2 }' | sed s/\"//g ) &&
ad5179780e25 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/ucsc-cell-browser/.shed.yml commit 2ba483354c14ddfd0f7aa57c2ad1c9944e9c4bba"
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32 echo "Study to replace: "\$study &&
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33 ## sed "s/ds=sample/ds=\$study/" '$__tool_directory__/redirect.html' > '$html_file';
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34 sed "s/ds=sample/ds=\$study/" '$redirect_html' > '$html_file';
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36 #else if $input_type.expression_source == "scanpy":
1b43a2d812c9 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/ucsc-cell-browser/.shed.yml commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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37
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38 ## We could add a condition here were, if cluster_field is provided
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39 ## then we rename it inside with an AnnData relying script to read 'louvain' to please UCSC CellBrowser
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41 ln -s '$input_anndata_file' scanpy_ann_data.h5ad;
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42 cbImportScanpy -i scanpy_ann_data.h5ad
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44 #if $input_type.marker_field:
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45 --markerField '${input_type.marker_field}'
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46 #end if
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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47
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48 #if $input_type.cluster_field:
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49 --clusterField '${input_type.cluster_field}'
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50 #end if
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52
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53 -o outdir -n sample --htmlDir '$html_file.extra_files_path';
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54 ## cp '$__tool_directory__/redirect.html' '$html_file';
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55 mv '$redirect_html' '$html_file';
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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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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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57 #end if
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58 ]]></command>
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59 <configfiles>
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60 <configfile name="redirect_html"><![CDATA[
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61 <!DOCTYPE HTML>
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62 <html lang="en-US">
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63 <head>
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64 <meta charset="UTF-8">
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65 <meta http-equiv="refresh" content="0; url=index.html?ds=sample">
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66 <script type="text/javascript">
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67 window.location.href = "index.html?ds=sample"
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68 </script>
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69 <title>Page Redirection</title>
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70 </head>
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71 <body>
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72 <!-- Note: don't tell people to `click` the link, just tell them that it is a link. -->
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73 If you are not redirected automatically, follow this <a href='index.html?ds=sample'>link to example</a>.
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74 </body>
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75 </html>
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76 ]]></configfile>
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77 </configfiles>
0
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78 <inputs>
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79 <conditional name="input_type">
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80 <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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81 <option value="native-cell-browser" selected="true">CellBrowser tar.gz expression matrix</option>
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82 <option value="scanpy">Scanpy AnnData HDF5 serialized object</option>
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83 <option value="cell-browser-tar">Tar file with CellBrowser files to execute cbBuild</option>
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84 </param>
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85 <when value="native-cell-browser">
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86 <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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87 <param type="data" name="cellMetadata" label="Cell metadata" help="Tabular file with metadata fields (columns) for each cell (rows)." format="tabular"/>
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88 <param type="data" name="tsneCoordinates" label="tSNE coordinates" help="Tabular file with tSNE coordinates for each cell." format="tabular"/>
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89 </when>
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90 <when value="cell-browser-tar">
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91 <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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92 </when>
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93 <when value="scanpy">
3
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94 <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."/>
5
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95 <param name="marker_field" argument="--markerField" type="text" value="rank_genes_groups" label="Marker genes field" help="Scanpy marker genes field to use (part of uns), optional, if not set 'rank_genes_groups' will be used."/>
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96 <param name="cluster_field" argument="--clusterField" type="text" label="Cluster field" help="Scanpy cluster field to use in obs. Optional, if not set 'louvain' will be used. If the AnnData object doesn't not have 'louvain' among its clustering fields in obs, then this NEEDS to be set or UCSC CellBrowser will fail."/>
0
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97 </when>
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98 </conditional>
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99 </inputs>
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100 <outputs>
3
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101 <data format="html" name="html_file" label="${tool.name} on ${on_string}: Interactive Viewer"/>
0
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102 </outputs>
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103
5
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104 <!-- Test data not included due to size, to obtain it execute get_test_data.sh -->
0
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105 <tests>
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106 <test>
5
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107 <conditional name="input_type">
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108 <param name="expression_source" value="scanpy"/>
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109 <param name="input_anndata_file" ftype="h5ad" value="E-MTAB-6077.project.h5ad"/>
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110 <param name="marker_field" value="markers_louvain_resolution_0.7"/>
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111 <param name="cluster_field" value="louvain_resolution_0.7"/>
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112 </conditional>
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113 <output name="html_file">
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114 <!-- mostly checking that execution doesn't fail, we cannot access the files
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115 with relevant content to check it -->
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116 <assert_contents>
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117 <has_text text="If you are not redirected automatically" />
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118 </assert_contents>
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119 </output>
0
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120 </test>
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121 </tests>
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122
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123 <help><![CDATA[
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124 UCSC Single Cell Browser
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125 ========================
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126
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127 Funded by the California Institute of Regenerative Medicine and the Chan-Zuckerberg
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128 Initiative https://www.chanzuckerberg.com/.
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129
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130 The UCSC Cell Browser is a viewer for single cell data. You can click on and hover
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131 over cells to get meta information, search for genes to color on and click clusters
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132 to show cluster-specific marker genes, which in turn are clickable again.
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133
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134 For a demo of the browser, see http://cells.ucsc.edu
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135
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136 Usage
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137 -----
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138
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139 After choosing the inputs and executing the tool, once the history item becomes
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140 green, press the View data (eye icon) button, which will open the generated UCSC Cell Browser
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141 interactive site.
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142
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143 For EBI Single Cell Expression Atlas AnnData files (available from http://ftp.ebi.ac.uk/pub/databases/microarray/data/atlas/sc_experiments/
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144 <accession> / <accession>.project.h5ad ), use `markers_louvain_resolution_<value>`
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145 for Marker genes fields and `louvain_resolution_<value>` for Cluster field. There will be different
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146 resolution values available, you can see them by executing `Inspect AnnData` tool, select
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147 and set "What to inspect" to "General information about the object". Then look in the results under
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148 obs and uns.
0
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149
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150 Troubleshooting
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151 ---------------
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152
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153 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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154 with the text "Choose cell...". If that is the case, close that panel (click on the cross)
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155 and then choose File -> Open Dataset... and then press the Open Dataset white button.
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156
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157 Version history
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158 ---------------
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159
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160 0.4.3+galaxy0: Initial contribution. Pablo Moreno, Expression Atlas team https://www.ebi.ac.uk/gxa/home at
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161 EMBL-EBI https://www.ebi.ac.uk/.
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162
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163 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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164 EMBL-EBI https://www.ebi.ac.uk/.
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165
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166 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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167 EMBL-EBI https://www.ebi.ac.uk/.
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168
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169 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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170 EMBL-EBI https://www.ebi.ac.uk/.
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171
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172 1.0.0+galaxy0: Update UCSC CellBrowser version to 1.0.0. Fixes bugs and improves support for AnnData objects. Pablo Moreno, Expression Atlas team https://www.ebi.ac.uk/gxa/home at
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173 EMBL-EBI https://www.ebi.ac.uk/.
0
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174 ]]></help>
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175 <citations>
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176 <citation type="bibtex">
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177 @misc{ucsc-cell-browser-gitrepo,
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178 author = {Maximilian Haeussler and collaborators},
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179 year = {2018},
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180 title = {UCSC Single Cell Browser: Python pipeline and Javascript scatter plot library for single-cell datasets},
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181 publisher = {GitHub},
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182 journal = {GitHub repository},
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183 url = {https://github.com/maximilianh/cellBrowser},
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184 }
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185 </citation>
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186 <citation type="doi">10.1038/s41592-021-01102-w</citation>
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187 <citation type="doi">10.1101/2020.10.30.361162</citation>
0
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188 </citations>
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189 </tool>