comparison scanpy-find-cluster.xml @ 16:5e68e130fafe draft

"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit e572b5425460d57f1bd13ab6374674c1c6801ab3-dirty"

15:ed07813a7266

<?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 )
    #elif $settings.resolution
        --resolution '${settings.resolution}'
    #end if
    #if $settings.restrict_to
        --restrict-to '${settings.restrict_to}'
    #end if
    #if $settings.use_weights

        <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"/>
        <param name="resolution_file" argument="--resolution" type="data" format="txt,tsv" optional="true"
               label="File with resolution, use with parameter iterator. Overrides the resolution setting"/>
        <param name="restrict_to" argument="--restrict-to" type="text" optional="true"

16:5e68e130fafe

<?xml version="1.0" encoding="utf-8"?>
<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 $settings.restrict_to
        --restrict-to '${settings.restrict_to}'
    #end if
    #if $settings.use_weights

        <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" 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"
               label="File with resolution, use with parameter iterator. Overrides the resolution setting"/>
        <param name="restrict_to" argument="--restrict-to" type="text" optional="true"