diff tools/protein_analysis/rxlr_motifs.xml @ 25:41a42022f815 draft

Uploaded v0.2.6, embedded citations

--- a/tools/protein_analysis/rxlr_motifs.xml	Tue Sep 17 12:06:15 2013 -0400
+++ b/tools/protein_analysis/rxlr_motifs.xml	Fri Nov 21 08:17:36 2014 -0500
@@ -1,8 +1,7 @@
-<tool id="rxlr_motifs" name="RXLR Motifs" version="0.0.7">
+<tool id="rxlr_motifs" name="RXLR Motifs" version="0.0.9">
     <description>Find RXLR Effectors of Plant Pathogenic Oomycetes</description>
     <command interpreter="python">
-      rxlr_motifs.py $fasta_file 8 $model $tabular_file
-      ##I want the number of threads to be a Galaxy config option...
+      rxlr_motifs.py "$fasta_file" "\$GALAXY_SLOTS" $model "$tabular_file"
     </command>
     <stdio>
         <!-- Anything other than zero is an error -->
@@ -176,4 +175,14 @@
 This wrapper is available to install into other Galaxy Instances via the Galaxy
 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp
     </help>
+    <citations>
+        <citation type="doi">10.7717/peerj.167</citation>
+        <!-- TODO - select from these citations depending on method picked -->
+        <citation type="doi">10.1038/nature06203</citation>
+        <citation type="doi">10.1105/tpc.107.051037</citation>
+        <citation type="doi">10.1371/journal.ppat.0020050</citation>
+        <citation type="doi">10.1101/gr.910003</citation>
+        <citation type="doi">10.1093/bioinformatics/14.9.755</citation>
+        <citation type="doi">10.1093/protein/10.1.1</citation>
+    </citations>
 </tool>