comparison monocle3-preprocess.xml @ 1:0869b0264af1 draft

planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 08ac0ad9182623944c4546f8ea8db6a1a537f7eb

0:384b9bcf2807

    --norm-method '${norm_method}'
#if $use_genes
    --use-genes '${use_genes}'
#end if
#if $residual_model_formula_str
    --residual-model-formula-str '~${residual_model_formula_str}'
#end if
#if $pseudo_count
    --pseudo-count '${pseudo_count}'
#end if
#if $no_scaling

    <param name="norm_method" argument="--norm-method" type="select" label="Determines how to transform expression values prior to reducing dimensionality.">
      <option value="log" selected="true">Size factor correction and log transformation</option>
      <option value="size_only">Size factor correction only</option>
    </param>
    <param name="use_genes" argument="--use-genes" type="text" optional="true" label="Manually subset the gene pool to these genes for dimensionality reduction."/>
    <param name="residual_model_formula_str" argument="--residual-model-formula-str" type="text" optional="true" label="A string model formula specifying effects to subtract from the data (excluding the leading ~)."/>
    <param name="pseudo_count" argument="--pseudo-count" optional="true" type="float" value="1" label="Amount to increase expression values before dimensionality reduction."/>
    <param name="no_scaling" argument="--no-scaling" type="boolean" checked="false" label="When this option is NOT set, scale each gene before running trajectory reconstruction."/>
    <expand macro="verbose_flag"/>
  </inputs>

1:0869b0264af1

    --norm-method '${norm_method}'
#if $use_genes
    --use-genes '${use_genes}'
#end if
#if $residual_model_formula_str
    --residual-model-formula-str '${residual_model_formula_str}'
#end if
#if $pseudo_count
    --pseudo-count '${pseudo_count}'
#end if
#if $no_scaling

    <param name="norm_method" argument="--norm-method" type="select" label="Determines how to transform expression values prior to reducing dimensionality.">
      <option value="log" selected="true">Size factor correction and log transformation</option>
      <option value="size_only">Size factor correction only</option>
    </param>
    <param name="use_genes" argument="--use-genes" type="text" optional="true" label="Manually subset the gene pool to these genes for dimensionality reduction."/>
    <param name="residual_model_formula_str" argument="--residual-model-formula-str" type="text" optional="true" label="A string model formula specifying effects to subtract from the data.">
      <sanitizer>
        <valid initial="string.printable"/>
      </sanitizer>
    </param>
    <param name="pseudo_count" argument="--pseudo-count" optional="true" type="float" value="1" label="Amount to increase expression values before dimensionality reduction."/>
    <param name="no_scaling" argument="--no-scaling" type="boolean" checked="false" label="When this option is NOT set, scale each gene before running trajectory reconstruction."/>
    <expand macro="verbose_flag"/>
  </inputs>