comparison seurat_run_tsne.xml @ 2:fd0fc93b3c87 draft

planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit bbe3c1f7fd8489951f2d90415fe80dd5cf961ca0

1:13a27436f8ee

<tool id="seurat_run_tsne" name="Seurat RunTSNE" version="@SEURAT_VERSION@_@VERSION@+galaxy0">
    <description>run t-SNE dimensionality reduction</description>
    <macros>
        <import>seurat_macros.xml</import>
    </macros>
    <expand macro="requirements" />

  --dim_embed '$adv.dim_embed'
#end if
#if $adv.random_seed
  --random-seed '$adv.random_seed'
#end if

@OUTPUT_OBJECT@
--output-embeddings-file output_embed
]]></command>

            </param>
            <param label="tSNE dimensions" optional="true" name="dim_embed" argument="--dim_embed" type="select" help="The dimensional space of the resulting tSNE embedding (default is 2). For example, set to 3 for a 3d tSNE">
              <option value="2" selected="true">2</option>
              <option value="3">3</option>
            </param>
            <param label="Random seed" optional="true" name="random_seed" argument="--random-seed" type="integer" help="Seed of the random number generator"/>
        </section>
    </inputs>

    <outputs>

2:fd0fc93b3c87

<tool id="seurat_run_tsne" name="Seurat RunTSNE" version="@SEURAT_VERSION@+galaxy1">
    <description>run t-SNE dimensionality reduction</description>
    <macros>
        <import>seurat_macros.xml</import>
    </macros>
    <expand macro="requirements" />

  --dim_embed '$adv.dim_embed'
#end if
#if $adv.random_seed
  --random-seed '$adv.random_seed'
#end if
#if $adv.perplexity
  --perplexity '$adv.perplexity'
#end if

@OUTPUT_OBJECT@
--output-embeddings-file output_embed
]]></command>

            </param>
            <param label="tSNE dimensions" optional="true" name="dim_embed" argument="--dim_embed" type="select" help="The dimensional space of the resulting tSNE embedding (default is 2). For example, set to 3 for a 3d tSNE">
              <option value="2" selected="true">2</option>
              <option value="3">3</option>
            </param>
            <param label="Perplexity" optional="true" name="perplexity" argument="--perplexity" type="integer" help="An integer above 0."/>
            <param label="Random seed" optional="true" name="random_seed" argument="--random-seed" type="integer" help="Seed of the random number generator"/>
        </section>
    </inputs>

    <outputs>