diff hyphy_fel.xml @ 0:24a2bf70dbdd draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/hyphy_fel.xml	Thu Jan 17 04:23:36 2019 -0500
@@ -0,0 +1,51 @@
+<?xml version="1.0"?>
+<tool id="hyphy_fel" name="HyPhy-FEL" version="@VERSION@+galaxy0">
+    <description>Fixed Effects Likelihood</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="version_command" />
+    <command detect_errors="exit_code">
+    <![CDATA[
+    ln -s '$input_file' fel_input.fa &&
+    ln -s '$input_nhx' fel_input.nhx &&
+    echo $gencodeid > tool_params &&
+    echo `pwd`/fel_input.fa >> tool_params &&
+    echo `pwd`/fel_input.nhx >> tool_params &&
+    echo '$branches' >> tool_params &&
+    echo '$include_srv' >> tool_params &&
+    echo '$p_value' >> tool_params &&
+    @HYPHY_INVOCATION@ \$HYPHY_LIB/TemplateBatchFiles/SelectionAnalyses/FEL.bf > '$fel_log'
+    ]]>
+    </command>
+    <inputs>
+        <expand macro="inputs" />
+        <expand macro="gencode" />
+        <expand macro="branches" />
+        <param name="p_value" type="float" value=".1" min="0" max="1" label="P-value" />
+        <param name="include_srv" type="select" label="Include synonymous rate variation">
+            <option value="1">Yes (recommended)</option>
+            <option value="2">No</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="fel_log" format="txt" />
+        <data name="fel_output" format="json" from_work_dir="fel_input.fa.FEL.json" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input_file" ftype="fasta" value="absrel-in1.fa" />
+            <param name="input_nhx" ftype="nhx" value="absrel-in1.nhx" />
+            <output name="fel_output" file="fel-out1.json" compare="sim_size" />
+        </test>
+    </tests>
+    <help>
+        <![CDATA[
+FEL (Fixed Effects Likelihood) uses a maximum-likelihood (ML) approach to infer nonsynoymous (dN) and synonymous (dS) substitution rates on a per-site basis for a given coding alignment and corresponding phylogeny. This method assumes that the selection pressure for each site is constant along the entire phylogeny.
+        ]]>
+    </help>
+    <expand macro="citations">
+        <citation type="doi">10.1093/molbev/msi105</citation>
+    </expand>
+</tool>