diff cell-browser.xml @ 0:1b43a2d812c9 draft

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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cell-browser.xml	Wed Apr 03 11:56:43 2019 -0400
@@ -0,0 +1,114 @@
+<tool id="ucsc_cell_browser" name="UCSC Cell Browser" version="0.4.38+galaxy0">
+  <description>displays single-cell clusterized data in an interactive web application.</description>
+  <requirements>
+    <requirement type="package" version="0.4.38">ucsc-cell-browser</requirement>
+  </requirements>
+<stdio>
+<exit_code range="1:" />
+</stdio>
+<command><![CDATA[
+#if $input_type.expression_source == "native-cell-browser":
+
+   echo "coords = [ {'file':'$tsneCoordinates', 'shortLabel':'t-SNE on WGCNA'} ]" > ./cellbrowser.conf;
+   echo "meta = '$cellMetadata'" >> ./cellbrowser.conf;
+   echo "name = 'sample'" >> ./cellbrowser.conf;
+   echo "exprMatrix = '$expressionMatrix'" >> ./cellbrowser.conf;
+   echo "geneIdType = 'symbol'" >> ./cellbrowser.conf;
+
+   cbBuild -i cellbrowser.conf -o "$html_file.extra_files_path";
+   mv "$html_file.extra_files_path"/index.html "$html_file";
+
+#else if $input_type.expression_source == "cell-browser-tar":
+
+   tar -xf '$tarred_sources';
+   cbBuild -i cellbrowser.conf -o "$html_file.extra_files_path";
+   mv "$html_file.extra_files_path"/index.html "$html_file";
+
+#else if $input_type.expression_source == "scanpy":
+
+   ln -s '$input_anndata_file' scanpy_ann_data.h5ad;
+   cbImportScanpy -i scanpy_ann_data.h5ad -o outdir -n sample --htmlDir "$html_file.extra_files_path";
+   mv "$html_file.extra_files_path"/index.html "$html_file";
+
+#end if
+]]></command>
+<inputs>
+  <conditional name="input_type">
+    <param type="select" name="expression_source" label="Choose the format of the expression data" help="Use compressed txt, Scanpy or Seurat objects">
+      <option value="native-cell-browser" selected="true">CellBrowser tar.gz expression matrix</option>
+      <option value="scanpy">Scanpy AnnData HDF5 serialized object</option>
+      <option value="cell-browser-tar">Tar file with CellBrowser files to execute cbBuild</option>
+    </param>
+    <when value="native-cell-browser">
+      <param type="data" name="expressionMatrix" label="Expression matrix" help="Tabular expression matrix (see https://github.com/maximilianh/cellBrowser/tree/master/sampleData)" format="tabular"/>
+      <param type="data" name="cellMetadata" label="Cell metadata" help="Tabular file with metadata fields (columns) for each cell (rows)." format="tabular"/>
+      <param type="data" name="tsneCoordinates" label="tSNE coordinates" help="Tabular file with tSNE coordinates for each cell." format="tabular"/>
+    </when>
+    <when value="cell-browser-tar">
+      <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"/>
+    </when>
+    <when value="scanpy">
+      <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."/>
+    </when>
+  </conditional>
+</inputs>
+<outputs>
+    <data format="html" name="html_file" label="Interactive UCSC Cell Browser"/>
+</outputs>
+
+<tests>
+  <test>
+    <param name="input_anndata_file" ftype="data" value="anndata.h5"/>
+    <output name="html_file" ftype="data" value="cellbrowser.html" compare="sim_size"/>
+  </test>
+</tests>
+
+<help><![CDATA[
+UCSC Single Cell Browser
+========================
+
+Funded by the California Institute of Regenerative Medicine and the Chan-Zuckerberg
+Initiative https://www.chanzuckerberg.com/.
+
+The UCSC Cell Browser is a viewer for single cell data. You can click on and hover
+over cells to get meta information, search for genes to color on and click clusters
+to show cluster-specific marker genes, which in turn are clickable again.
+
+For a demo of the browser, see http://cells.ucsc.edu
+
+Usage
+-----
+
+After choosing the inputs and executing the tool, once the history item becomes
+green, press the View data (eye icon) button, which will open the generated UCSC Cell Browser
+interactive site. Press the white on blue "Open Dataset" button.
+
+Troubleshooting
+---------------
+
+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
+with the text "Choose cell...". If that is the case, close that panel (click on the cross)
+and then choose File -> Open Dataset... and then press the Open Dataset white button.
+
+Version history
+---------------
+
+0.4.3+galaxy0: Initial contribution. Pablo Moreno, Expression Atlas team https://www.ebi.ac.uk/gxa/home  at
+EMBL-EBI https://www.ebi.ac.uk/.
+
+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
+EMBL-EBI https://www.ebi.ac.uk/.
+]]></help>
+<citations>
+ <citation type="bibtex">
+  @misc{ucsc-cell-browser-gitrepo,
+  author = {Maximilian Haeussler and collaborators},
+  year = {2018},
+  title = {UCSC Single Cell Browser: Python pipeline and Javascript scatter plot library for single-cell datasets},
+  publisher = {GitHub},
+  journal = {GitHub repository},
+  url = {https://github.com/maximilianh/cellBrowser},
+ }
+ </citation>
+</citations>
+</tool>