diff tools/clinod/clinod.xml @ 4:4d9a4a43861b draft

Uploaded v0.0.7, uses $GALAXY_SLOTS and embeds citation in tool XML.

--- a/tools/clinod/clinod.xml	Wed Sep 18 06:09:33 2013 -0400
+++ b/tools/clinod/clinod.xml	Thu Nov 20 06:15:49 2014 -0500
@@ -1,4 +1,4 @@
-<tool id="clinod" name="Nucleolar localization sequence Detector (NoD)" version="0.0.5">
+<tool id="clinod" name="Nucleolar localization sequence Detector (NoD)" version="0.0.7">
     <description>Find nucleolar localization signals (NoLSs) in protein sequences</description>
     <requirements>
         <requirement type="binary">java</requirement>
@@ -7,8 +7,7 @@
     <command>
 ##The Galaxy Tool Shed installation should define $CLINOD to point at folder
 ##containing both clinod-1.3.jar and the batchman binary:
-java -jar \$CLINOD/clinod-1.3.jar -in="$fasta_file" -out="$tabular_file" -t=2 -f=MEDIUM_TAB -nonols -clean_sequence
-##I want the number of threads to be a Galaxy config option...
+java -jar \$CLINOD/clinod-1.3.jar -in="$fasta_file" -out="$tabular_file" -t="\$GALAXY_SLOTS" -f=MEDIUM_TAB -nonols -clean_sequence
 ##TODO - Make the -clean_sequence argument a parameter?
     </command>
     <stdio>
@@ -25,7 +24,7 @@
     <tests>
         <test>
             <param name="fasta_file" value="four_human_proteins.fasta" ftype="fasta" />
-	    <output name="tabular_file" file="four_human_proteins.clinod-1.3.tabular" ftype="tabular" />
+            <output name="tabular_file" file="four_human_proteins.clinod-1.3.tabular" ftype="tabular" />
         </test>
     </tests>
     <help>
@@ -82,4 +81,9 @@
 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/clinod
 
     </help>
+    <citations>
+        <citation type="doi">10.7717/peerj.167</citation>
+        <citation type="doi">10.1093/nar/gkq653</citation>
+        <citation type="doi">10.1186/1471-2105-12-317</citation>
+    </citations>
 </tool>