diff hyphy_meme.xml @ 2:e44501a5cdcc draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty

--- a/hyphy_meme.xml	Mon Sep 10 15:14:49 2018 -0400
+++ b/hyphy_meme.xml	Tue Oct 30 10:57:16 2018 -0400
@@ -8,13 +8,14 @@
     <version_command>HYPHYMP --version | tail -n 1 | awk '{print $1}'</version_command>
     <command detect_errors="exit_code">
     <![CDATA[
+    export MPI_NODE_COUNT=\${GALAXY_SLOTS:-1} &&
     ln -s '$input_file' meme_input.fa &&
     ln -s '$input_nhx' meme_input.nhx &&
     echo $gencodeid > tool_params &&
     echo `pwd`/meme_input.fa >> tool_params &&
     echo `pwd`/meme_input.nhx >> tool_params &&
-    echo '$branches' >> tool_params &&
-    echo '$p_value' >> tool_params &&
+    echo $branches >> tool_params &&
+    echo $p_value >> tool_params &&
     @HYPHY_INVOCATION@ \$HYPHY_LIB/TemplateBatchFiles/SelectionAnalyses/MEME.bf > '$meme_log'
     ]]>
     </command>
@@ -35,6 +36,20 @@
             <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>
@@ -49,14 +64,16 @@
     </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="input_file" ftype="fasta" value="meme-in1.fa" />
+            <param name="input_nhx" ftype="nhx" value="meme-in1.nhx" />
+            <param name="branches" value="1" />
+            <param name="p_value" value="0.1" />
             <output name="meme_output" file="meme-out1.json" compare="sim_size" />
         </test>
     </tests>
     <help>
         <![CDATA[
-Detecting  natural selection within protein coding genes is difficult to identify because selection is frequently transient or episodic. Existing computational techniques, which are designed to identify sites subject to pervasive selection, may fail to recognize sites where selection is episodic. MEME is capable of identifying instances of both episodic and pervasive positive selection at the level of an individual site.
+MEME employs a mixed-effects maximum likelihood approach to test the hypothesis that individual sites have been subject to episodic positive or diversifying selection. In other words,  MEME aims to detect sites evolving under positive selection under a proportion of branches.
         ]]>
     </help>
     <expand macro="citations">