Mercurial > repos > dktanwar > test_fgsea_1

diff 16_fgsea/GSEA.xml~ @ 0:b75ceb945966 draft

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author dktanwar
date Mon, 11 Dec 2017 09:52:26 -0500
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/16_fgsea/GSEA.xml~	Mon Dec 11 09:52:26 2017 -0500
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+<tool id="GSEA" name="Gene Set Enrichment Analysis" version="0.1.0">
+  <command detect_errors="exit_code"><![CDATA[
+        RScript $__tool_directory__/GSEA.R --input1 $Ranked_list --input2 $Pathway_database --output $output
+    ]]></command>
+  <inputs>
+    <param type="data" name="Ranked_list" format="txt" />
+    <param type="data" name="Pathway_database" format="txt" />
+  </inputs>
+  <outputs>
+    <data name="Results" format="txt" />
+  </outputs>
+  <tests>
+    <test>
+      <param name="Ranked_list" value="ranked_genes_list.rnk"/>
+      <param name="Pathway_database" value="ouse.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>