comparison scanpy-run-tsne.xml @ 15:b5e1939cc155 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"

14:c4a20a57d825

<?xml version="1.0" encoding="utf-8"?>
<tool id="scanpy_run_tsne" name="Scanpy RunTSNE" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
  <description>visualise cell clusters using tSNE</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-run-tsne
#if $use_rep != "auto"
    --use-rep '${use_rep}'
#end if
#if $key_added
    --key-added '${key_added}'
#end if
#if $embeddings
    --export-embedding embeddings.tsv
#end if
#if $settings.default == "false"
    #if $settings.perplexity_file
        --perplexity \$( cat $settings.perplexity_file )
    #else
        --perplexity '${settings.perplexity}'
    #end if
    --early-exaggeration '${settings.early_exaggeration}'
    --learning-rate '${settings.learning_rate}'
    #if $settings.n_pc
        --n-pcs ${settings.n_pc}

        --random-state ${settings.random_seed}
    #end if
#end if
    @INPUT_OPTS@
    @OUTPUT_OPTS@

]]></command>

  <inputs>
    <expand macro="input_object_params"/>

    <param name="use_rep" argument="--use-rep" type="select" label="Use the indicated representation">
      <option value="X_pca">X_pca, use PCs</option>
      <option value="X">X, use normalised expression values</option>
      <option value="auto" selected="true">Automatically chosen based on problem size</option>
    </param>
    <param name="key_added" argument="--key-added" type="text" optional="true"
           label="Additional suffix to the name of the slot to save the embedding"/>

    <conditional name="settings">
      <param name="default" type="boolean" checked="true" label="Use programme defaults"/>
      <when value="true"/>
      <when value="false">
        <param name="perplexity" argument="--perplexity" type="float" value="30" label="The perplexity is related to the number of nearest neighbours, select a value between 5 and 50"/>
        <param name="perplexity_file" argument="--perplexity" type="data" format="txt,tsv" label="The perplexity is related to the number of nearest neighbours" help="For use with the parameter iterator. Overrides the persplexity option above" optional="true"/>
        <param name="early_exaggeration" argument="--early-exaggeration" type="float" value="12" label="Controls the tightness within and between clusters"/>
        <param name="learning_rate" argument="--learning-rate" type="float" value="1000" label="Learning rate, should be between 100 and 1000"/>
        <param name="fast_tsne" type="boolean" checked="false" label="Use multicoreTSNE" help="Depending on the setup and version, the availability of the needed library might vary and hence fail."/>

15:b5e1939cc155

<?xml version="1.0" encoding="utf-8"?>
<tool id="scanpy_run_tsne" name="Scanpy RunTSNE" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
  <description>visualise cell clusters using tSNE</description>
  <macros>
    <import>scanpy_macros2.xml</import>
  </macros>
  <expand macro="requirements"/>
  <command detect_errors="exit_code"><![CDATA[
#from pathlib import Path
#set embeddings_tsv='embeddings.tsv'
ln -s '${input_obj_file}' input.h5 &&
PYTHONIOENCODING=utf-8 scanpy-run-tsne
#if $use_rep != "auto"
    --use-rep '${use_rep}'
#end if
#if $embeddings
    --export-embedding embeddings.tsv
#end if
#if $settings.default == "false"
    #if $settings.perplexity_file
        #set perplexity = Path($settings.perplexity_file.__str__).read_text().strip()
    #elif $settings.perplexity
        #set perplexity = $settings.perplexity.__str__.strip()
    #end if      
    #if $perplexity
        --perplexity '$perplexity'
    #end if
    #if $settings.key_added
        #set key_added = $settings.key_added
        #if $perplexity
            #set key_added = $key_added.replace('PERPLEXITY', $perplexity.__str__)
        #end if
        --key-added '${key_added}'
        #set embeddings_tsv="embeddings_" + $key_added.__str__ + ".tsv"    
    #end if
    --early-exaggeration '${settings.early_exaggeration}'
    --learning-rate '${settings.learning_rate}'
    #if $settings.n_pc
        --n-pcs ${settings.n_pc}

        --random-state ${settings.random_seed}
    #end if
#end if
    @INPUT_OPTS@
    @OUTPUT_OPTS@
#if $embeddings
    #if $embeddings_tsv != 'embeddings.tsv'
        && mv '${embeddings_tsv}' embeddings.tsv
    #end if
#end if

]]></command>

  <inputs>
    <expand macro="input_object_params"/>

    <param name="use_rep" argument="--use-rep" type="select" label="Use the indicated representation">
      <option value="X_pca">X_pca, use PCs</option>
      <option value="X">X, use normalised expression values</option>
      <option value="auto" selected="true">Automatically chosen based on problem size</option>
    </param>
    <conditional name="settings">
      <param name="default" type="boolean" checked="true" label="Use programme defaults"/>
      <when value="true"/>
      <when value="false">
        <param name="key_added" argument="--key-added" type="text" optional="true"
               label="Additional suffix to the name of the slot to save the embedding" help="If included, PERPLEXITY will be substituted with the value of the perplexity setting."/>
        <param name="perplexity" argument="--perplexity" type="float" value="30" label="The perplexity is related to the number of nearest neighbours, select a value between 5 and 50"/>
        <param name="perplexity_file" argument="--perplexity" type="data" format="txt,tsv" label="The perplexity is related to the number of nearest neighbours" help="For use with the parameter iterator. Overrides the persplexity option above" optional="true"/>
        <param name="early_exaggeration" argument="--early-exaggeration" type="float" value="12" label="Controls the tightness within and between clusters"/>
        <param name="learning_rate" argument="--learning-rate" type="float" value="1000" label="Learning rate, should be between 100 and 1000"/>
        <param name="fast_tsne" type="boolean" checked="false" label="Use multicoreTSNE" help="Depending on the setup and version, the availability of the needed library might vary and hence fail."/>