diff raxml.xml @ 2:a4b71be30c3c draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit 9f9e37b75ae2e5735289eeec1c74ff49e6e388e0"

--- a/raxml.xml	Tue Jun 27 16:27:39 2017 -0400
+++ b/raxml.xml	Mon Dec 02 07:52:10 2019 -0500
@@ -1,7 +1,8 @@
-<tool id="raxml" name="Phyogenetic reconstruction with RaXML" version="8.2.4">
+<tool id="raxml" name="Phyogenetic reconstruction with RaXML" version="8.2.4+galaxy1">
     <description>- Maximum Likelihood based inference of large phylogenetic trees</description>
     <requirements>
         <requirement type="package" version="8.2.4">raxml</requirement>
+        <requirement type="package" version="3.6">python</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
 ## binary is hard-coded to the pthreads enabled raxml executable if threads > 1
@@ -447,8 +448,8 @@
             <param name="infile" value="dna.phy"/>
             <param name="model_type" value="nucleotide"/>
             <param name="base_model" value="GTRCAT"/>
-            <output name="parsimonyTreeReq" file="RAxML_parsimonyTree.galaxy.basic" />
-            <output name="bestTree">
+            <output name="parsimonyTreeReq" file="RAxML_parsimonyTree.galaxy.basic" ftype="nhx" />
+            <output name="bestTree" ftype="nhx">
                 <assert_contents>
                     <has_text_matching expression="Frog" />
                 </assert_contents>
@@ -460,14 +461,13 @@
             <param name="model_type" value="nucleotide"/>
             <param name="base_model" value="GTRCAT"/>
             <param name="number_of_runs" value="5"/>
-            <output name="parsimonyTree">
+            <output name="parsimonyTree" ftype="nhx">
                 <assert_contents>
                     <has_text_matching expression="Chicken" />
-                    <has_text_matching expression="RUN.4" />
                 </assert_contents>
             </output>
-            <output name="parsimonyTreeReq" file="RAxML_parsimonyTree.galaxy.multi" lines_diff="30"/>
-            <output name="bestTree">
+            <output name="parsimonyTreeReq" file="RAxML_parsimonyTree.galaxy.multi" ftype="nhx"/>
+            <output name="bestTree" ftype="nhx">
                 <assert_contents>
                     <has_text_matching expression="Whale" />
                 </assert_contents>