Mercurial > repos > ebi-gxa > ucsc_cell_browser

annotate cell-browser.xml @ 2:cc47d8df79eb 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 f12604f7ae850f2269a924f95a442c668948a61a"
author ebi-gxa
date Thu, 11 Jun 2020 20:58:35 +0000
parents 92a98e92907f
children
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cc47d8df79eb "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 f12604f7ae850f2269a924f95a442c668948a61a"
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1 <tool id="ucsc_cell_browser" name="UCSC Cell Browser" version="0.7.10+galaxy0" 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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cc47d8df79eb "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 f12604f7ae850f2269a924f95a442c668948a61a"
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4 <requirement type="package" version="0.7.10">ucsc-cell-browser</requirement>
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5 </requirements>
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6 <stdio>
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7 <exit_code range="1:" />
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8 </stdio>
1838f77608a6 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 0a95e950ac73efdc9e84025ecb547e66fc3b83f6
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9 <command><![CDATA[
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10 #if $input_type.expression_source == "native-cell-browser":
1838f77608a6 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/ucsc-cell-browser/.shed.yml commit 0a95e950ac73efdc9e84025ecb547e66fc3b83f6
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92a98e92907f "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/ucsc-cell-browser/.shed.yml commit 2ba483354c14ddfd0f7aa57c2ad1c9944e9c4bba"
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12 echo "coords = [ {'file':'$tsneCoordinates', 'shortLabel':'t-SNE'} ]" > ./cellbrowser.conf;
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13 echo "meta = '$cellMetadata'" >> ./cellbrowser.conf;
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14 echo "name = 'sample'" >> ./cellbrowser.conf;
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15 echo "exprMatrix = '$expressionMatrix'" >> ./cellbrowser.conf;
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16 echo "geneIdType = 'symbol'" >> ./cellbrowser.conf;
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18 cbBuild -i cellbrowser.conf -o "$html_file.extra_files_path";
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92a98e92907f "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/ucsc-cell-browser/.shed.yml commit 2ba483354c14ddfd0f7aa57c2ad1c9944e9c4bba"
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20 ## "sample" is used as name, so no change needed.
92a98e92907f "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/ucsc-cell-browser/.shed.yml commit 2ba483354c14ddfd0f7aa57c2ad1c9944e9c4bba"
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21 cp '$__tool_directory__/redirect.html' '$html_file';
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23 #else if $input_type.expression_source == "cell-browser-tar":
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25 tar -xf '$tarred_sources';
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26 cbBuild -i cellbrowser.conf -o "$html_file.extra_files_path";
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28 ## we need to adapt redirect to use the study name used in cellbrowser.conf
92a98e92907f "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 $2 }' | sed s/\"//g ) &&
92a98e92907f "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/ucsc-cell-browser/.shed.yml commit 2ba483354c14ddfd0f7aa57c2ad1c9944e9c4bba"
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30 echo "Study to replace: "\$study &&
92a98e92907f "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/ucsc-cell-browser/.shed.yml commit 2ba483354c14ddfd0f7aa57c2ad1c9944e9c4bba"
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31 sed "s/ds=sample/ds=\$study/" '$__tool_directory__/redirect.html' > '$html_file';
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33 #else if $input_type.expression_source == "scanpy":
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34
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35 ## We could add a condition here were, if cluster_field is provided
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36 ## then we rename it inside with an AnnData relying script to read 'louvain' to please UCSC CellBrowser
92a98e92907f "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/ucsc-cell-browser/.shed.yml commit 2ba483354c14ddfd0f7aa57c2ad1c9944e9c4bba"
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37
0
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38 ln -s '$input_anndata_file' scanpy_ann_data.h5ad;
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39 cbImportScanpy -i scanpy_ann_data.h5ad
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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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44
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cc47d8df79eb "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 f12604f7ae850f2269a924f95a442c668948a61a"
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45 #if $input_type.cluster_field:
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46 --clusterField '${input_type.cluster_field}'
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47 #end if
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cc47d8df79eb "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 f12604f7ae850f2269a924f95a442c668948a61a"
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49
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92a98e92907f "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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50 -o outdir -n sample --htmlDir '$html_file.extra_files_path';
92a98e92907f "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/ucsc-cell-browser/.shed.yml commit 2ba483354c14ddfd0f7aa57c2ad1c9944e9c4bba"
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51 cp '$__tool_directory__/redirect.html' '$html_file';
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53 #end if
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54 ]]></command>
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55 <inputs>
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56 <conditional name="input_type">
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57 <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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58 <option value="native-cell-browser" selected="true">CellBrowser tar.gz expression matrix</option>
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59 <option value="scanpy">Scanpy AnnData HDF5 serialized object</option>
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60 <option value="cell-browser-tar">Tar file with CellBrowser files to execute cbBuild</option>
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61 </param>
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62 <when value="native-cell-browser">
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63 <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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64 <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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65 <param type="data" name="tsneCoordinates" label="tSNE coordinates" help="Tabular file with tSNE coordinates for each cell." format="tabular"/>
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66 </when>
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67 <when value="cell-browser-tar">
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68 <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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69 </when>
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70 <when value="scanpy">
1
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71 <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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72 <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."/>
2
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73 <param name="cluster_field" argument="--clusterField" type="text" label="Cluster field" help="Scanpy cluster field to use. Optional, if not set 'louvain' will be used. If the AnnData object doesn't not have 'louvain' among its clustering fields, then this NEEDS to be set or UCSC CellBrowser will fail."/>
0
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74 </when>
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75 </conditional>
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76 </inputs>
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77 <outputs>
1
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78 <data format="html" name="html_file" label="${tool.name} on ${on_string}: Interactive Viewer"/>
0
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79 </outputs>
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80
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81 <tests>
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82 <test>
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83 <param name="input_anndata_file" ftype="data" value="anndata.h5"/>
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84 <output name="html_file" ftype="data" value="cellbrowser.html" compare="sim_size"/>
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85 </test>
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86 </tests>
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87
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88 <help><![CDATA[
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89 UCSC Single Cell Browser
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90 ========================
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91
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92 Funded by the California Institute of Regenerative Medicine and the Chan-Zuckerberg
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93 Initiative https://www.chanzuckerberg.com/.
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94
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95 The UCSC Cell Browser is a viewer for single cell data. You can click on and hover
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96 over cells to get meta information, search for genes to color on and click clusters
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97 to show cluster-specific marker genes, which in turn are clickable again.
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98
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99 For a demo of the browser, see http://cells.ucsc.edu
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100
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101 Usage
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102 -----
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103
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104 After choosing the inputs and executing the tool, once the history item becomes
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105 green, press the View data (eye icon) button, which will open the generated UCSC Cell Browser
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106 interactive site. Press the white on blue "Open Dataset" button.
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107
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108 Troubleshooting
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109 ---------------
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110
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111 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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112 with the text "Choose cell...". If that is the case, close that panel (click on the cross)
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113 and then choose File -> Open Dataset... and then press the Open Dataset white button.
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114
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115 Version history
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116 ---------------
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117
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118 0.4.3+galaxy0: Initial contribution. 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/.
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120
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121 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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122 EMBL-EBI https://www.ebi.ac.uk/.
1
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123
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124 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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125 EMBL-EBI https://www.ebi.ac.uk/.
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126
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127 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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128 EMBL-EBI https://www.ebi.ac.uk/.
0
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129 ]]></help>
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130 <citations>
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131 <citation type="bibtex">
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132 @misc{ucsc-cell-browser-gitrepo,
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133 author = {Maximilian Haeussler and collaborators},
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134 year = {2018},
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135 title = {UCSC Single Cell Browser: Python pipeline and Javascript scatter plot library for single-cell datasets},
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136 publisher = {GitHub},
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137 journal = {GitHub repository},
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138 url = {https://github.com/maximilianh/cellBrowser},
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139 }
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140 </citation>
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92a98e92907f "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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141 <citation type="doi">10.1101/2020.04.08.032698</citation>
0
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142 </citations>
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143 </tool>