Repository revision
23:621d7d7a605f

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

Scanpy FindCluster tool metadata
Miscellaneous
based on community detection on KNN graph
scanpy_find_cluster
toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_find_cluster/scanpy_find_cluster/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_find_cluster/scanpy_find_cluster/1.8.1+galaxy0
toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_find_cluster/scanpy_find_cluster/1.7.2+galaxy0 (this tool)
toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_find_cluster/scanpy_find_cluster/1.6.0+galaxy4
toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_find_cluster/scanpy_find_cluster/1.6.0+galaxy3
toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_find_cluster/scanpy_find_cluster/1.6.0+galaxy2
toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_find_cluster/scanpy_find_cluster/1.6.0+galaxy1
toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_find_cluster/scanpy_find_cluster/1.6.0+galaxy0
toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_find_cluster/scanpy_find_cluster/1.4.3+galaxy11
toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_find_cluster/scanpy_find_cluster/1.4.3+galaxy10
toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_find_cluster/scanpy_find_cluster/1.4.3+galaxy9
toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_find_cluster/scanpy_find_cluster/1.4.3+galaxy8
toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_find_cluster/scanpy_find_cluster/1.4.3+galaxy6
toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_find_cluster/scanpy_find_cluster/1.4.3+galaxy1
toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_find_cluster/scanpy_find_cluster/1.4.2+galaxy1
toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_find_cluster/scanpy_find_cluster/1.3.2+galaxy1
scanpy_find_cluster
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-find-cluster
    ${method}
#if $settings.default == "false"
    #if $settings.resolution_file
        #set f = open($settings.resolution_file.__str__)
        #set resolution = f.read().strip()
        #silent f.close
    #elif $settings.resolution
        #set resolution = $settings.resolution.__str__.strip()
    #end if

    --neighbors-key '${settings.neighbors_key}'
    #if $settings.key_added
        #set key_added = $settings.key_added.replace('METHOD', $method.__str__)
        #if $resolution
            #set key_added = $key_added.replace('RESOLUTION', $resolution.__str__)
        #end if
        --key-added '${key_added}'
    #end if
    #if $resolution
        --resolution '$resolution'
    #end if
    #if $settings.layer
        --layer '${settings.layer}'
    #end if
    #if $settings.restrict_to
        --restrict-to '${settings.restrict_to}'
    #end if
    #if $settings.use_weights
        --use-weights
    #end if
    --random-state '${settings.random_seed}'
    ${settings.directed}
#end if
#if $output_cluster
    --export-cluster output.tsv
#end if
    
    --input-format '${input_format}' input.h5
  
    
#if str($output_format).startswith('anndata')
    --show-obj stdout --output-format anndata output.h5
#else
    --show-obj stdout --output-format loom output.h5
#end if
  
None
False
False
Functional tests
name inputs outputs required files
Test-1 input_obj_file: compute_graph.h5
input_format: anndata
output_format: anndata
settings|resolution_file: resolution.txt
settings|random_seed: 0
settings|default: False
name: value
name: value
compute_graph.h5
resolution.txt
value
Test-2 input_obj_file: compute_graph.h5
input_format: anndata
output_format: anndata
settings|resolution: 1.0
settings|random_seed: 0
settings|default: False
name: value
name: value
compute_graph.h5
value
Test-3 input_obj_file: compute_graph.h5
input_format: anndata
output_format: anndata
method: louvain
settings|key_added: METHOD_RESOLUTION
settings|resolution: 1.0
settings|random_seed: 0
settings|default: False
name: value
name: value
compute_graph.h5
value