Mercurial > repos > ebi-gxa > sc3_estimate_k

diff sc3-estimate-k.xml @ 0:aab4d3a52ee3 draft default tip

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planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
author ebi-gxa
date Wed, 03 Apr 2019 11:25:01 -0400
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/sc3-estimate-k.xml	Wed Apr 03 11:25:01 2019 -0400
@@ -0,0 +1,41 @@
+<?xml version="1.0" encoding="utf-8"?>
+<tool id="sc3_estimate_k" name="SC3 Estimate" version="@TOOL_VERSION@+galaxy0">
+  <description>the number of clusters for k-means clustering</description>
+  <macros>
+    <import>sc3-macros.xml</import>
+  </macros>
+  <expand macro="requirements" />
+  <command detect_errors="exit_code"><![CDATA[
+sc3-sc3-estimate-k.R -i '${sc3_prepared}' -t '${sc3_estimated_k}' -o sc3_estimated.rds &&
+
+echo -n "estimated k = " && cat ${sc3_estimated_k}
+  ]]></command>
+
+  <inputs>
+    <param type="data" name="sc3_prepared" format="rdata" label="Serialised sc3 SingleCellExperiment object"/>
+  </inputs>
+
+  <outputs>
+    <data name="sc3_estimated_k" format="txt" label="${tool.name} on ${on_string}: txt file containting estimated K value"/>
+  </outputs>
+
+  <tests>
+    <test>
+      <param name="sc3_prepared" value="sc3_prepared.rds"/>
+      <output name="sc3_estimated_k" file="sc3-estimated-k.txt"/>
+    </test>
+  </tests>
+
+  <help><![CDATA[
+========================================================================================
+Uses Tracy-Widom theory on random matrices to estimate the optimal number of clusters k.
+========================================================================================
+
+It creates and populates the k_estimation item of the sc3 slot of the metadata(object).
+
+@HELP@
+
+@VERSION_HISTORY@
+  ]]></help>
+  <expand macro="citations" />
+</tool>