diff hyphy_fel.xml @ 1:6c3ece5fb602 draft

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

--- a/hyphy_fel.xml	Thu Jan 17 04:23:36 2019 -0500
+++ b/hyphy_fel.xml	Wed Aug 21 12:27:42 2019 -0400
@@ -4,47 +4,43 @@
     <macros>
         <import>macros.xml</import>
     </macros>
-    <expand macro="requirements" />
-    <expand macro="version_command" />
-    <command detect_errors="exit_code">
-    <![CDATA[
-    ln -s '$input_file' fel_input.fa &&
-    ln -s '$input_nhx' fel_input.nhx &&
-    echo $gencodeid > tool_params &&
-    echo `pwd`/fel_input.fa >> tool_params &&
-    echo `pwd`/fel_input.nhx >> tool_params &&
-    echo '$branches' >> tool_params &&
-    echo '$include_srv' >> tool_params &&
-    echo '$p_value' >> tool_params &&
-    @HYPHY_INVOCATION@ \$HYPHY_LIB/TemplateBatchFiles/SelectionAnalyses/FEL.bf > '$fel_log'
-    ]]>
-    </command>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+        ln -s '$input_file' fel_input.fa &&
+        ln -s '$input_nhx' fel_input.nhx &&
+        @HYPHY_INVOCATION@ fel
+            --alignment ./fel_input.fa
+            --tree ./fel_input.nhx
+            --code '$gencodeid'
+            --branches '$branches'
+            --srv '$include_srv'
+            --pvalue '$p_value'
+            > '$fel_log'
+    ]]></command>
     <inputs>
-        <expand macro="inputs" />
-        <expand macro="gencode" />
-        <expand macro="branches" />
-        <param name="p_value" type="float" value=".1" min="0" max="1" label="P-value" />
+        <expand macro="inputs"/>
+        <expand macro="gencode"/>
+        <expand macro="branches"/>
+        <param name="p_value" type="float" value=".1" min="0" max="1" label="P-value"/>
         <param name="include_srv" type="select" label="Include synonymous rate variation">
-            <option value="1">Yes (recommended)</option>
-            <option value="2">No</option>
+            <option value="Yes">Yes (recommended)</option>
+            <option value="No">No</option>
         </param>
     </inputs>
     <outputs>
-        <data name="fel_log" format="txt" />
-        <data name="fel_output" format="json" from_work_dir="fel_input.fa.FEL.json" />
+        <data name="fel_log" format="txt"/>
+        <data name="fel_output" format="hyphy_results.json" from_work_dir="fel_input.fa.FEL.json"/>
     </outputs>
     <tests>
         <test>
-            <param name="input_file" ftype="fasta" value="absrel-in1.fa" />
-            <param name="input_nhx" ftype="nhx" value="absrel-in1.nhx" />
-            <output name="fel_output" file="fel-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"/>
+            <output name="fel_output" file="fel-out1.json" compare="sim_size"/>
         </test>
     </tests>
-    <help>
-        <![CDATA[
+    <help><![CDATA[
 FEL (Fixed Effects Likelihood) uses a maximum-likelihood (ML) approach to infer nonsynoymous (dN) and synonymous (dS) substitution rates on a per-site basis for a given coding alignment and corresponding phylogeny. This method assumes that the selection pressure for each site is constant along the entire phylogeny.
-        ]]>
-    </help>
+    ]]></help>
     <expand macro="citations">
         <citation type="doi">10.1093/molbev/msi105</citation>
     </expand>