diff 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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/sc3-calc-transfs.xml	Wed Apr 03 11:34:00 2019 -0400
@@ -0,0 +1,46 @@
+<?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>