diff hyphy_absrel.xml @ 1:5c87e4907e08 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"

--- a/hyphy_absrel.xml	Thu Jan 17 04:22:13 2019 -0500
+++ b/hyphy_absrel.xml	Wed Aug 21 12:24:13 2019 -0400
@@ -4,47 +4,40 @@
     <macros>
         <import>macros.xml</import>
     </macros>
-    <expand macro="requirements" />
-    <expand macro="version_command" />
-    <command detect_errors="exit_code">
-    <![CDATA[
-    ln -s '$input_file' absrel_input.fa &&
-    ln -s '$input_nhx' absrel_input.nhx &&
-    echo $gencodeid > tool_params &&
-    echo `pwd`/absrel_input.fa >> tool_params &&
-    echo `pwd`/absrel_input.nhx >> tool_params &&
-    echo '$branches' >> tool_params &&
-    @HYPHY_INVOCATION@ \$HYPHY_LIB/TemplateBatchFiles/SelectionAnalyses/aBSREL.bf
-    #if $log:
-        > '$absrel_log'
-    #end if
-    ]]>
-    </command>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+        ln -s '$input_file' absrel_input.fa &&
+        ln -s '$input_nhx' absrel_input.nhx &&
+        @HYPHY_INVOCATION@ absrel
+            --alignment ./absrel_input.fa
+            --tree ./absrel_input.nhx
+            --code '$gencodeid'
+            --branches '$branches'
+            > '$absrel_log'
+        ]]></command>
     <inputs>
-        <expand macro="inputs" />
-        <param name="log" type="boolean" truevalue="" falsevalue="" label="Output aBSREL log to history" />
-        <expand macro="gencode" />
-        <expand macro="branches" />
+        <expand macro="inputs"/>
+        <param name="log" type="boolean" truevalue="" falsevalue="" label="Output aBSREL log to history"/>
+        <expand macro="gencode"/>
+        <expand macro="branches"/>
     </inputs>
     <outputs>
         <data name="absrel_log" format="txt">
             <filter>log</filter>
         </data>
-        <data name="absrel_output" format="json" from_work_dir="absrel_input.fa.ABSREL.json" />
+        <data name="absrel_output" format="hyphy_results.json" from_work_dir="absrel_input.fa.ABSREL.json"/>
     </outputs>
     <tests>
         <test>
-            <param name="input_file" ftype="fasta" value="absrel-in1.fa" />
-            <param name="input_nhx" ftype="nhx" value="absrel-in1.nhx" />
-            <param name="log" value="false" />
-            <output name="absrel_output" file="absrel-out1.json" compare="sim_size" />
+            <param name="input_file" ftype="fasta" value="absrel-in1.fa"/>
+            <param name="input_nhx" ftype="nhx" value="absrel-in1.nhx"/>
+            <param name="log" value="false"/>
+            <output name="absrel_output" file="absrel-out1.json" compare="sim_size"/>
         </test>
     </tests>
-    <help>
-        <![CDATA[
+    <help><![CDATA[
 aBSREL (Adaptive branch-site random effects likelihood) uses an adaptive random effects branch-site model framework to test whether each branch has evolved under positive selection, using a procedure which infers an optimal number of rate categories per branch.
-        ]]>
-    </help>
+    ]]></help>
     <expand macro="citations">
         <citation type="doi">10.1093/molbev/msv022</citation>
     </expand>