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changeset 1:23f1abdec8d1 draft default tip

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Uploaded
author dktanwar
date Mon, 18 Dec 2017 21:10:26 -0500
parents 3a53b8e91ede
children
files GSEA.xml
diffstat 1 files changed, 42 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/GSEA.xml	Mon Dec 18 21:10:26 2017 -0500
@@ -0,0 +1,42 @@
+<tool id="GSEA" name="Gene Set Enrichment Analysis" version="0.1.0">
+  
+<requirements>
+  <requirement type="package" version="1.4.0">bioconductor-fgsea</requirement>
+  <requirement type="package" version="1.20.0">r-getopt</requirement>
+  <!-- required for alpha function used with plotMD -->
+  <requirement type="package" version="0.12.13">r-rcpp</requirement>
+  <requirement type="package" version="1.10.4">r-data.table</requirement>
+</requirements>
+
+<command detect_errors="exit_code"><![CDATA[
+        Rscript '$__tool_directory__/GSEA.R' --input1 '$edgeR_output' --input2 '$Pathway_database' --output '$output'
+    ]]></command>
+  <inputs>
+    <param type="data" name="edgeR_output" format="tabular" />
+    <param type="data" name="Pathway_database" format="txt" />
+  </inputs>
+  <outputs>
+    <data name="output" format="txt" />
+  </outputs>
+  <tests>
+    <test>
+      <param name="edgeR_output" value="input.tab"/>
+      <param name="Pathway_database" value="mouse.gmt"/>
+      <output name="output" file="GSEA_results.txt"/>
+    </test>
+  </tests>
+  <help><![CDATA[
+        Write the tool help section here.
+    ]]></help>
+  <citations>
+    <citation type="bibtex">
+      @misc{github01_mismatch_removal,
+      author = {LastTODO, FirstTODO},
+      year = {TODO},
+      title = {01_mismatch_removal},
+      publisher = {GitHub},
+      journal = {GitHub repository},
+      url = {https://github.com/dktanwar/Galaxy_Tools/tree/master/01_mismatch_removal},
+      }</citation>
+  </citations>
+</tool>