diff hyphy_relax.xml @ 0:551616a65f8f draft

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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/hyphy_relax.xml	Wed Aug 21 12:24:55 2019 -0400
@@ -0,0 +1,53 @@
+<?xml version="1.0"?>
+<tool id="hyphy_relax" name="HyPhy-RELAX" version="@VERSION@+galaxy0">
+    <description>Detect relaxed selection in a codon-based
+    phylogenetic framework</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+        ln -s '$input_file' relax_input.fa &&
+        ln -s '$input_nhx' relax_input.nhx &&
+        @HYPHY_INVOCATION@ relax
+            --alignment ./relax_input.fa
+            --tree ./relax_input.nhx
+            --models '$analysisType'
+            #if $treeAnnotations == "2":
+                --test TEST
+                --reference REFERENCE
+            #else:
+                --test TEST
+            #end if
+            > '$relax_log'
+    ]]></command>
+    <inputs>
+        <expand macro="inputs"/>
+        <expand macro="gencode"/>
+        <param name="analysisType" type="select" label="Analysis Type">
+            <option value="All">All</option>
+            <option value="Minimal">Minimal</option>
+        </param>
+        <param name="treeAnnotations" type="select" label="Tree Annotations">
+            <option value="1">TEST only</option>
+            <option value="2">TEST and REFERENCE</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="relax_log" format="txt"/>
+        <data name="relax_output" format="hyphy_results.json" from_work_dir="relax_input.fa.RELAX.json"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input_file" ftype="fasta" value="relax-in1.fa"/>
+            <param name="input_nhx" ftype="nhx" value="relax-in1.nhx"/>
+            <output name="relax_output" file="relax-out1.json" compare="sim_size"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+RELAX (Detect relaxed selection in a codon-based phylogenetic framework)
+    ]]></help>
+    <expand macro="citations">
+        <citation type="doi">10.1093/molbev/msu400</citation>
+    </expand>
+</tool>