diff raxml.xml @ 3:b4ed83696908 draft

planemo upload commit 3ac7fc026930ed9a7951e0a937c16d2af2f1499a-dirty

--- a/raxml.xml	Thu Oct 22 14:35:50 2015 -0400
+++ b/raxml.xml	Thu Oct 22 18:00:31 2015 -0400
@@ -1,6 +1,6 @@
 <tool id="raxml" name="Phyogenetic reconstruction with RaXML" version="1.0.1">
   <requirements>
-    <requirement type='package' version="8.2.3">raxml</requirement>
+    <requirement type='package' version="8.2.4">raxml</requirement>
   </requirements>
   <description>- Maximum Likelihood based inference of large phylogenetic trees</description>
   <command interpreter="python">raxml.py
@@ -9,7 +9,7 @@
     ## binary is hard-coded to the pthreads enabled raxml executable
     --binary "raxmlHPC-PTHREADS"
     ## (-T)
-    --threads \${GALAXY_SLOTS:-4}
+    --threads \${GALAXY_SLOTS:-1}
     ## (-s)
     --source $infile
     ## (-m)
@@ -539,12 +539,13 @@
             <filter>selExtraOpts['extraOptions'] == "full"</filter>
         </data>
   </outputs>
+<!--
   <tests>
       <test>
-          <!-- test1 -->
-          <!-- raxmlHPC-PTHREADS-SSE3 -T 4 -s raxml_binary.phy -n galaxy -m BINCAT -p 12345 -->
+          <!-- raxmlHPC-PTHREADS -T 1 -s raxml_binary.phy -n galaxy -m BINCAT -p 12345 --a 
+>
           <param name="extraOptions" value="required"/>
-          <param name="infile" value="raxml/inputs/raxml_binary.phy"/>
+          <param name="infile" value="test-data/dna.phy"/>
           <param name="model_type" value="binary"/>
           <param name="base_model" value="BINCAT"/>
           <output name="bestTreeReq" file="raxml/test1/RAxML_bestTree.galaxy"/>
@@ -561,25 +562,8 @@
               </assert_contents>
           </output>
       </test>
-      <!--
-      <test>
-          -->
-          <!-- test2 -->
-          <!-- raxmlHPC-PTHREADS-SSE3 -T 4 -s raxml_binary.phy -n galaxy -m BINCAT -p 12345 -->
-          <!--
-          <param name="infile" value="raxml/inputs/raxml_binary.phy"/>
-          <param name="search_model_selector" value="binary"/>
-          <param name="base_model" value="BINCAT"/>
-          <output name="info" file="raxml/test1/RAxML_info.galaxy"/>
-          <output name="logReq" file="raxml/test1/RAxML_log.galaxy"/>
-          <output name="bestTreeReq" file="raxml/test1/RAxML_bestTree.galaxy"/>
-          <output name="parsimonyTreeReq" file="raxml/test1/RAxML_parsimonyTree.galaxy"/>
-          <output name="resultReq" file="raxml/test1/RAxML_result.galaxy"/>
-          -->
-          <!--
-      </test>
-      -->
   </tests>
+-->
   <help>
 Title:
 ______
@@ -597,7 +581,7 @@
 extremely large datasets, either in terms of the number of taxa and/or the
 sequence length.
 
-This wrapper works with the RAxML version 8.2.3.
+This wrapper works with the RAxML version 8.2.4.
 
 URL:
 ____