Mercurial > repos > rdvelazquez > hyphy_fade

diff hyphy_fade.xml @ 9:4377e155b9d1 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6c73b2e4c05bdddaef2026feb1073c1b0b4aa12e-dirty
author rdvelazquez
date Fri, 07 Jun 2019 10:18:47 -0400
parents a7305e34418f
children
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line diff
--- a/hyphy_fade.xml	Mon Feb 18 15:11:29 2019 -0500
+++ b/hyphy_fade.xml	Fri Jun 07 10:18:47 2019 -0400
@@ -1,41 +1,27 @@
 <?xml version="1.0"?>
-<tool id="hyphy_fade" name="HyPhy-FADE" version="@VERSION@+galaxy0">
+<tool id="hyphy_fade" name="HyPhy-FADE" version="2.5.0+galaxy0">
   <description>: FUBAR* Approach to Directional Evolution (*Fast
   Unconstrained Bayesian Approximation)</description>
   <macros>
     <import>macros.xml</import>
   </macros>
   <expand macro="requirements"/>
-  <version_command>HYPHYMP --version | tail -n 1 | awk '{print
-  $1}'</version_command>
   <command detect_errors="exit_code"><![CDATA[
-    #if $posteriorEstimationMethod == 3:
-      ln -s '$input_file' fade_input.fa &&
-      ln -s '$input_nhx' fade_input.nhx &&
-      echo `pwd`/fade_input.fa >> tool_params &&
-      echo `pwd`/fade_input.nhx >> tool_params &&
-      echo '$branches' >> tool_params &&
-      echo '$grid_points' >> tool_params &&
-      echo '$substitutionmodel' >> tool_params &&
-      echo '$posteriorEstimationMethod' >> tool_params &&
-      echo '$concentration' >> tool_params &&
-      @HYPHY_INVOCATION@ \$HYPHY_LIB/TemplateBatchFiles/SelectionAnalyses/FADE.bf > '$fade_log'
-    #else:
-      ln -s '$input_file' fade_input.fa &&
-      ln -s '$input_nhx' fade_input.nhx &&
-      echo `pwd`/fade_input.fa >> tool_params &&
-      echo `pwd`/fade_input.nhx >> tool_params &&
-      echo '$branches' >> tool_params &&
-      echo '$grid_points' >> tool_params &&
-      echo '$substitutionmodel' >> tool_params &&
-      echo '$posteriorEstimationMethod' >> tool_params &&
-      echo '$mcmc' >> tool_params &&
-      echo '$chain_length' >> tool_params &&
-      echo '$samples' >> tool_params &&
-      echo '$samples_per_chain' >> tool_params &&
-      echo '$concentration' >> tool_params &&
-      @HYPHY_INVOCATION@ \$HYPHY_LIB/TemplateBatchFiles/SelectionAnalyses/FADE.bf > '$fade_log'
-    #end if
+    ln -s '$input_file' fade_input.fa &&
+    ln -s '$input_nhx' fade_input.nhx &&
+    @HYPHY_INVOCATIN@ fade
+      --alignment `pwd`/fade_input.fa
+      --tree `pwd`/fade_input.nhx
+      --branches '$branches'
+      --model '$substitutionmodel'
+      --method '$posteriorEstimationMethod'
+      --grid '$grid_points'
+      --concentration_parameter '$concentration'
+      --chains '$mcmc'
+      --chain-length '$chain_length'
+      --burn-in '$samples'
+      --samples '$samples_per_chain'
+      > '$fade_log'
     ]]></command>
   <inputs>
     <param name="input_file" type="data" format="fasta" label="Input amino acid FASTA file"/>