diff hyphy_meme.xml @ 3:3b7f2dbb5c44 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6e7f074d80e0f35516e223b76e73f019ad45dd74-dirty

--- a/hyphy_meme.xml	Tue Oct 30 10:57:16 2018 -0400
+++ b/hyphy_meme.xml	Wed Mar 06 14:31:33 2019 -0500
@@ -5,7 +5,7 @@
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements" />
-    <version_command>HYPHYMP --version | tail -n 1 | awk '{print $1}'</version_command>
+    <expand macro="version_command" />
     <command detect_errors="exit_code">
     <![CDATA[
     export MPI_NODE_COUNT=\${GALAXY_SLOTS:-1} &&
@@ -20,47 +20,14 @@
     ]]>
     </command>
     <inputs>
-        <param name="input_file" type="data" format="fasta" label="Input FASTA file" />
-        <param name="input_nhx" type="data" format="nhx" label="Input newick file" />
-        <param name="gencodeid" type="select" label="Genetic code">
-            <option value="1">Universal code</option>
-            <option value="2">Vertebrate mitochondrial DNA code</option>
-            <option value="3">Yeast mitochondrial DNA code</option>
-            <option value="4">Mold, Protozoan and Coelenterate mt; Mycloplasma/Spiroplasma</option>
-            <option value="5">Invertebrate mitochondrial DNA code</option>
-            <option value="6">Ciliate, Dasycladacean and Hexamita Nuclear code</option>
-            <option value="7">Echinoderm mitochondrial DNA code</option>
-            <option value="8">Euplotid Nuclear code</option>
-            <option value="9">Alternative Yeast Nuclear code</option>
-            <option value="10">Ascidian mitochondrial DNA code</option>
-            <option value="11">Flatworm mitochondrial DNA code</option>
-            <option value="12">Blepharisma Nuclear code</option>
-        </param>
-        <conditional name="rate_cond">
-            <param name="rate" type="select" label="Rate variation">
-                <option value="1">None</option>
-                <option value="2">General Discrete</option>
-                <option value="3">Beta-Gamma</option>
-            </param>
-            <when value="1" />
-            <when value="2">
-                <param name="rate_classes" type="integer" value="2" min="2" max="6" label="Rate classes" />
-            </when>
-            <when value="3">
-                <param name="rate_classes" type="integer" value="2" min="2" max="6" label="Rate classes" />
-            </when>
-        </conditional>
-        <param name="branches" type="select" label="Set of branches to test">
-            <option value="1">All branches</option>
-            <option value="2">Internal branches</option>
-            <option value="3">Leaf branches</option>
-            <option value="4">Unlabeled branches</option>
-        </param>
+        <expand macro="inputs" />
+        <expand macro="gencode" />
+        <expand macro="branches" />
         <param name="p_value" type="float" value=".1" min="0" max="1" label="P-value" />
     </inputs>
     <outputs>
         <data name="meme_log" format="txt" />
-        <data name="meme_output" format="json" from_work_dir="meme_input.fa.MEME.json" />
+        <data name="meme_output" format="hyphy_json_results" from_work_dir="meme_input.fa.MEME.json" />
     </outputs>
     <tests>
         <test>