comparison scanpy-find-cluster.xml @ 13:c46750e2e4a4 draft

"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 62f47287c7e8449c59a1f1f454852ddc669b1b1e-dirty"

12:b456d129066d

<?xml version="1.0" encoding="utf-8"?>
<tool id="scanpy_find_cluster" name="Scanpy FindCluster" version="@TOOL_VERSION@+galaxy11" 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 $settings.default == "false"
    --use-graph '${settings.use_graph}'
    #if $settings.key_added
        --key-added '${settings.key_added}'
    #end if
    #if $settings.resolution_file
        --resolution \$( cat $settings.resolution_file )

    <conditional name="settings">
      <param name="default" type="boolean" checked="true" label="Use programme defaults"/>
      <when value="true"/>
      <when value="false">
        <param name="use_graph" argument="--use-graph" value="neighbors" type="text"
            label="Name of the slot that holds the KNN graph"/>
        <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"/>

        <param name="resolution" argument="--resolution" type="float" min="0.0" value="1.0"
               label="Resolution, high value for more and smaller clusters"/>

13:c46750e2e4a4

<?xml version="1.0" encoding="utf-8"?>
<tool id="scanpy_find_cluster" name="Scanpy FindCluster" version="@TOOL_VERSION@+galaxy0" 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 $settings.default == "false"
    --neighbors-key '${settings.neighbors_key}'
    #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 )

    <conditional name="settings">
      <param name="default" type="boolean" checked="true" label="Use programme defaults"/>
      <when value="true"/>
      <when value="false">
        <param name="neighbors_key" argument="--neighbors-key" value="neighbors" type="text"
            label="Name of the slot that holds the KNN graph"/>
        <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"/>

        <param name="resolution" argument="--resolution" type="float" min="0.0" value="1.0"
               label="Resolution, high value for more and smaller clusters"/>