comparison scanpy-find-cluster.xml @ 19:b531acda966c draft

"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 0fc0cc467014e750dbaa6c47b528b25af0bdc0c4-dirty"

18:15e8a4c60418

<?xml version="1.0" encoding="utf-8"?>
<tool id="scanpy_find_cluster" name="Scanpy FindCluster" version="@TOOL_VERSION@+galaxy3" 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[
#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

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__)

19:b531acda966c

<?xml version="1.0" encoding="utf-8"?>
<tool id="scanpy_find_cluster" name="Scanpy FindCluster" version="@TOOL_VERSION@+galaxy4" 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[
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__)