comparison cell-browser.xml @ 4:8da642e17794 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 f12604f7ae850f2269a924f95a442c668948a61a"

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 $input_type.marker_field:
     --markerField '${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>

      <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"/>

4:8da642e17794

<tool id="ucsc_cell_browser" name="UCSC Cell Browser" version="0.7.10+galaxy0" profile="18.01">
  <description>displays single-cell clusterized data in an interactive web application.</description>
  <requirements>
    <requirement type="package" version="0.7.10">ucsc-cell-browser</requirement>
  </requirements>
<stdio>
<exit_code range="1:" />
</stdio>
<command><![CDATA[

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

   #if $input_type.cluster_field:
     --clusterField '${input_type.cluster_field}'
   #end if


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

#end if
]]></command>

      <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."/>
      <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."/>
    </when>
  </conditional>
</inputs>
<outputs>
    <data format="html" name="html_file" label="${tool.name} on ${on_string}: Interactive Viewer"/>