annotate sc3-calc-transfs.xml @ 0:b06019da7b5a draft default tip

planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4

<?xml version="1.0" encoding="utf-8"?>
<tool id="sc3_calc_transfs" name="SC3 Calculate Transformations" version="@TOOL_VERSION@+galaxy0">
  <description>of distances using PCA and graph Laplacian</description>
  <macros>
    <import>sc3-macros.xml</import>
  </macros>
  <expand macro="requirements" />
  <command detect_errors="exit_code"><![CDATA[
sc3-sc3-calc-transfs.R -i '${sc3_distances}' -o '${sc3_transformed}'
  ]]></command>

  <inputs>
    <param name="sc3_distances" type="data" format="rdata" label="Serialised sc3 SingleCellExperiment object with distances calculated"/>
  </inputs>

  <outputs>
    <data name="sc3_transformed" format="rdata" label="${tool.name} on ${on_string}: serialised sc3 SingleCellExperiment object with transformed distances"/>
  </outputs>

  <tests>
    <test>
      <param name="sc3_distances" value="sc3_distances.rdata"/>
      <output name="sc3_transformed" file="sc3_transformed.rdata"/>
    </test>
  </tests>

  <help><![CDATA[
==============================================
This function calculate transformed distances.
==============================================

All items of the sc3 slot of the metadata(object) are transformed using either
principal component analysis (PCA) or by calculating the eigenvectors of the
associated graph Laplacian. The columns of the resulting matrices are then
sorted in descending order by their corresponding eigenvalues. The first d
columns (where d = max(metadata(object)$sc3$n_dim)) of each transformation are
then written to the transformations item of the sc3 slot. Additionally, this
function also removes the previously calculated distances from the sc3 slot, as
they are not needed for further analysis.

@HELP@

@VERSION_HISTORY@
    ]]></help>
    <expand macro="citations" />
</tool>