comparison scanpy-run-tsne.xml @ 12:dccd544c21ca 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"

11:a597590ccf6c

<?xml version="1.0" encoding="utf-8"?>
<tool id="scanpy_run_tsne" name="Scanpy RunTSNE" version="@TOOL_VERSION@+galaxy10" profile="@PROFILE@">
  <description>visualise cell clusters using tSNE</description>
  <macros>
    <import>scanpy_macros2.xml</import>
  </macros>
  <expand macro="requirements"/>

#end if
#if $key_added
    --key-added '${key_added}'
#end if
#if $embeddings
    --export-embedding embeddings.csv
#end if
#if $settings.default == "false"
    #if $settings.perplexity_file
        --perplexity \$( cat $settings.perplexity_file )
    #else

]]></command>

  <inputs>
    <expand macro="input_object_params"/>
    <expand macro="output_object_params"/>
    <param name="embeddings" type="boolean" checked="true" label="Output embeddings in csv format"/>

    <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>

  </inputs>

  <outputs>
    <expand macro="output_data_obj" description="tSNE object"/>
    <data name="output_embed" format="csv" from_work_dir="embeddings.csv" label="${tool.name} on ${on_string}: tSNE embeddings">
      <filter>embeddings</filter>
    </data>
  </outputs>

  <tests>

      <param name="output_format" value="anndata"/>
      <param name="default" value="false"/>
      <param name="embeddings" value="true"/>
      <param name="random_seed" value="0"/>
      <output name="output_h5" file="run_tsne.h5" ftype="h5" compare="sim_size"/>
      <output name="output_embed" file="run_tsne.embeddings.csv" ftype="csv" compare="sim_size">
        <assert_contents>
          <has_n_columns n="2" sep=","/>
        </assert_contents>
      </output>
    </test>
  </tests>

12:dccd544c21ca

<?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"/>

#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

]]></command>

  <inputs>
    <expand macro="input_object_params"/>
    <expand macro="output_object_params"/>
    <param name="embeddings" type="boolean" checked="true" label="Output embeddings in tsv format"/>

    <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>

  </inputs>

  <outputs>
    <expand macro="output_data_obj" description="tSNE object"/>
    <data name="output_embed" format="tabular" from_work_dir="embeddings.tsv" label="${tool.name} on ${on_string}: tSNE embeddings">
      <filter>embeddings</filter>
    </data>
  </outputs>

  <tests>

      <param name="output_format" value="anndata"/>
      <param name="default" value="false"/>
      <param name="embeddings" value="true"/>
      <param name="random_seed" value="0"/>
      <output name="output_h5" file="run_tsne.h5" ftype="h5" compare="sim_size"/>
      <output name="output_embed" file="run_tsne.embeddings.tsv" ftype="tabular" compare="sim_size">
        <assert_contents>
          <has_n_columns n="3"/>
        </assert_contents>
      </output>
    </test>
  </tests>