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diff hyphy_absrel.xml @ 0:419cd817299c draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
author iuc
date Thu, 17 Jan 2019 04:22:13 -0500
parents
children 5c87e4907e08
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/hyphy_absrel.xml	Thu Jan 17 04:22:13 2019 -0500
@@ -0,0 +1,51 @@
+<?xml version="1.0"?>
+<tool id="hyphy_absrel" name="HyPhy-aBSREL" version="@VERSION@+galaxy0">
+    <description>adaptive Branch Site Random Effects Likelihood</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="version_command" />
+    <command detect_errors="exit_code">
+    <![CDATA[
+    ln -s '$input_file' absrel_input.fa &&
+    ln -s '$input_nhx' absrel_input.nhx &&
+    echo $gencodeid > tool_params &&
+    echo `pwd`/absrel_input.fa >> tool_params &&
+    echo `pwd`/absrel_input.nhx >> tool_params &&
+    echo '$branches' >> tool_params &&
+    @HYPHY_INVOCATION@ \$HYPHY_LIB/TemplateBatchFiles/SelectionAnalyses/aBSREL.bf
+    #if $log:
+        > '$absrel_log'
+    #end if
+    ]]>
+    </command>
+    <inputs>
+        <expand macro="inputs" />
+        <param name="log" type="boolean" truevalue="" falsevalue="" label="Output aBSREL log to history" />
+        <expand macro="gencode" />
+        <expand macro="branches" />
+    </inputs>
+    <outputs>
+        <data name="absrel_log" format="txt">
+            <filter>log</filter>
+        </data>
+        <data name="absrel_output" format="json" from_work_dir="absrel_input.fa.ABSREL.json" />
+    </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="log" value="false" />
+            <output name="absrel_output" file="absrel-out1.json" compare="sim_size" />
+        </test>
+    </tests>
+    <help>
+        <![CDATA[
+aBSREL (Adaptive branch-site random effects likelihood) uses an adaptive random effects branch-site model framework to test whether each branch has evolved under positive selection, using a procedure which infers an optimal number of rate categories per branch.
+        ]]>
+    </help>
+    <expand macro="citations">
+        <citation type="doi">10.1093/molbev/msv022</citation>
+    </expand>
+</tool>