Repository revision
17:9fafbfcdee0d

Repository 'scanpy_plot_embed'
hg clone https://toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_plot_embed

Scanpy PlotEmbed tool metadata
Miscellaneous
visualise cell embeddings
scanpy_plot_embed
toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_plot_embed/scanpy_plot_embed/1.7.2+galaxy0
1.7.2+galaxy0
None
True
Version lineage of this tool (guids ordered most recent to oldest)
toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_plot_embed/scanpy_plot_embed/1.8.1+galaxy0
toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_plot_embed/scanpy_plot_embed/1.7.2+galaxy0 (this tool)
toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_plot_embed/scanpy_plot_embed/1.6.0+galaxy0
toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_plot_embed/scanpy_plot_embed/1.4.3+galaxy10
toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_plot_embed/scanpy_plot_embed/1.4.3+galaxy9
toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_plot_embed/scanpy_plot_embed/1.4.3+galaxy8
toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_plot_embed/scanpy_plot_embed/1.4.3+galaxy6
toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_plot_embed/scanpy_plot_embed/1.4.3+galaxy1
toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_plot_embed/scanpy_plot_embed/1.4.3+galaxy0
toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_plot_embed/scanpy_plot_embed/1.4.2+galaxy0
scanpy_plot_embed
Requirements (dependencies defined in the <requirements> tag set)
name version type
scanpy-scripts 0.4.0 package
Additional information about this tool
ln -s '${input_obj_file}' input.h5 &&
PYTHONIOENCODING=utf-8 scanpy-cli plot embed

    --input-format '${input_format}' input.h5
  
#if $color_by
    --color '${color_by}'
#end if
${use_raw}
    --legend-loc '${legend_loc}'
    --legend-fontsize '${legend_fontsize}'
#if $basis
    --basis '${basis}'
#end if
#if $groups
    --groups $groups
#end if
#if $neighbors_key
    --neighbors-key '${neighbors_key}'
#end if    
#if $layer
    --layer '${layer}'
#end if
#if $point_size
    --size ${point_size}
#end if
#if $gene_symbols_field
    --gene-symbols ${gene_symbols_field}
    #end if
${edges} --edges-width ${edges_width}
#if $edges_color
    --edges-color ${edges_color}
#end if
#if $components
    --components ${components}
#end if
--projection $projection
$sort_order

#if $fig_title
    --title '${fig_title}'
#end if
    --fig-size '${fig_size}'
    --fig-dpi ${fig_dpi}
    --fig-fontsize ${fig_fontsize}
    ${fig_frame}
    ./output.png
  
None
False
False
Functional tests
name inputs outputs required files
Test-1 input_obj_file: find_cluster.h5
input_format: anndata
basis: X_pca
color_by: louvain
use_raw: False
name: value
find_cluster.h5
value