| Previous changeset 15:ed07813a7266 (2020-09-11) Next changeset 17:b45b85d5c7ec (2020-09-29) |
|
Commit message:
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit e572b5425460d57f1bd13ab6374674c1c6801ab3-dirty" |
|
modified:
scanpy-find-cluster.xml |
| b |
| diff -r ed07813a7266 -r 5e68e130fafe scanpy-find-cluster.xml --- a/scanpy-find-cluster.xml Fri Sep 11 11:01:02 2020 +0000 +++ b/scanpy-find-cluster.xml Thu Sep 17 16:24:22 2020 +0000 |
| [ |
| @@ -1,27 +1,36 @@ <?xml version="1.0" encoding="utf-8"?> -<tool id="scanpy_find_cluster" name="Scanpy FindCluster" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@"> +<tool id="scanpy_find_cluster" name="Scanpy FindCluster" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@"> <description>based on community detection on KNN graph</description> <macros> <import>scanpy_macros2.xml</import> </macros> <expand macro="requirements"/> <command detect_errors="exit_code"><![CDATA[ +#from pathlib import Path +#if $settings.resolution_file + #set resolution = Path($settings.resolution_file.__str__).read_text().strip() +#elif $settings.resolution + #set resolution = $settings.resolution.__str__.strip() +#end if + ln -s '${input_obj_file}' input.h5 && PYTHONIOENCODING=utf-8 scanpy-find-cluster ${method} #if $settings.default == "false" --neighbors-key '${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 $settings.key_added - --key-added '${settings.key_added}' - #end if - #if $settings.resolution_file - --resolution \$( cat $settings.resolution_file ) - #elif $settings.resolution - --resolution '${settings.resolution}' - #end if #if $settings.restrict_to --restrict-to '${settings.restrict_to}' #end if @@ -57,8 +66,7 @@ <param name="layer" argument="--layer" value="" type="text" label="Key from adata.layers whose value will be used to perform tests on. (Default: use .X)"/> <param name="key_added" argument="--key-added" type="text" optional="true" - label="Additional suffix to the name of the slot to save the calculated clustering"/> - + label="Additional suffix to the name of the slot to save the calculated clustering" help="If included, the keyword 'METHOD' will be substituted with the value of the method setting and 'RESOLUTION' with the value of that field."/> <param name="resolution" argument="--resolution" type="float" min="0.0" value="1.0" label="Resolution, high value for more and smaller clusters"/> <param name="resolution_file" argument="--resolution" type="data" format="txt,tsv" optional="true" |