comparison cell-browser.xml @ 3:ad5179780e25 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 2ba483354c14ddfd0f7aa57c2ad1c9944e9c4bba"

2:679dfd1dd63b

<tool id="ucsc_cell_browser" name="UCSC Cell Browser" version="0.5.43+galaxy0">
  <description>displays single-cell clusterized data in an interactive web application.</description>
  <requirements>
    <requirement type="package" version="0.5.43">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">

    </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"/>

  publisher = {GitHub},
  journal = {GitHub repository},
  url = {https://github.com/maximilianh/cellBrowser},
 }
 </citation>
</citations>
</tool>

3:ad5179780e25

<tool id="ucsc_cell_browser" name="UCSC Cell Browser" version="0.5.43+galaxy1" profile="18.01">
  <description>displays single-cell clusterized data in an interactive web application.</description>
  <requirements>
    <requirement type="package" version="0.5.43">ucsc-cell-browser</requirement>
  </requirements>
<stdio>
<exit_code range="1:" />
</stdio>
<command><![CDATA[
#if $input_type.expression_source == "native-cell-browser":

   echo "coords = [ {'file':'$tsneCoordinates', 'shortLabel':'t-SNE'} ]" > ./cellbrowser.conf;
   echo "meta = '$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";

   ## "sample" is used as name, so no change needed.
   cp '$__tool_directory__/redirect.html' '$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";

   ## we need to adapt redirect to use the study name used in cellbrowser.conf
   study=\$(grep '^name=' cellbrowser.conf | awk -F'=' '{ print $2 }' | sed s/\"//g ) &&
   echo "Study to replace: "\$study &&
   sed "s/ds=sample/ds=\$study/" '$__tool_directory__/redirect.html' > '$html_file';

#else if $input_type.expression_source == "scanpy":

   ## We could add a condition here were, if cluster_field is provided
   ## then we rename it inside with an AnnData relying script to read 'louvain' to please UCSC CellBrowser

   ln -s '$input_anndata_file' scanpy_ann_data.h5ad;
   cbImportScanpy -i scanpy_ann_data.h5ad

   #if $input_type.marker_field:
     --markerField '${input_type.marker_field}'
   #end if

     -o outdir -n sample --htmlDir '$html_file.extra_files_path';
   cp '$__tool_directory__/redirect.html' '$html_file';

#end if
]]></command>
<inputs>
  <conditional name="input_type">

    </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,h5ad" label="Input object in AnnData hdf5 format" help="Scanpy serialized output is by default produced as an AnnData hdf5 file."/>
      <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."/>
    </when>
  </conditional>
</inputs>
<outputs>
    <data format="html" name="html_file" label="${tool.name} on ${on_string}: Interactive Viewer"/>
</outputs>

<tests>
  <test>
    <param name="input_anndata_file" ftype="data" value="anndata.h5"/>

  publisher = {GitHub},
  journal = {GitHub repository},
  url = {https://github.com/maximilianh/cellBrowser},
 }
 </citation>
 <citation type="doi">10.1101/2020.04.08.032698</citation>
</citations>
</tool>