diff map_ensembl_transcripts.xml @ 0:2c498d40ecde

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/map_ensembl_transcripts.xml	Mon Apr 09 12:03:06 2012 -0400
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+<tool id="gd_new_oscar" name="Map" version="1.0.0">
+  <description>Ensembl transcripts to KEGG pathways</description>
+
+  <command interpreter="python">
+    rtrnKEGGpthwfENSEMBLTc.py
+      "--loc_file=${GALAXY_DATA_INDEX_DIR}/gd.oscar.loc"
+      "--species=${input.metadata.dbkey}"
+      "--input=${input}"
+      "--posENSEMBLclmn=${ensembl_col}"
+      "--output=${output}"
+  </command>
+
+  <inputs>
+    <param name="input" type="data" format="tabular" label="Table" />
+    <param name="ensembl_col" type="data_column" data_ref="input" label="Column with ENSEMBL transcript code" />
+  </inputs>
+
+  <outputs>
+    <data name="output" format="tabular" />
+  </outputs>
+
+  <!--
+  <tests>
+    <test>
+      <param name="input" value="test_in/ensembl.tabular" ftype="tabular">
+        <metadata name="dbkey" value="canFam2" />
+      </param>
+      <param name="ensembl_col" value="1" />
+
+      <output name="output" file="test_out/map_ensembl_transcripts/map_ensembl_transcripts.tabular" />
+    </test>
+  </tests>
+  -->
+
+  <help>
+**What it does**
+
+Adds the fields KEGG gene codes and KEGG pathways to an input table of ENSEMBL transcript codes.
+  </help>
+</tool>