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comparison hyphy_slac.xml @ 0:9da003917dcb 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 04:24:25 -0500
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1 <?xml version="1.0"?>
2 <tool id="hyphy_slac" name="HyPhy-SLAC" version="@VERSION@+galaxy0">
3 <description>Single Likelihood Ancestor Counting</description>
4 <macros>
5 <import>macros.xml</import>
6 </macros>
7 <expand macro="requirements" />
8 <expand macro="version_command" />
9 <command detect_errors="exit_code">
10 <![CDATA[
11 ln -s '$input_file' slac_input.fa &&
12 ln -s '$input_nhx' slac_input.nhx &&
13 echo $gencodeid > tool_params &&
14 echo `pwd`/slac_input.fa >> tool_params &&
15 echo `pwd`/slac_input.nhx >> tool_params &&
16 echo '$branches' >> tool_params &&
17 echo '$number_of_samples' >> tool_params &&
18 echo '$p_value' >> tool_params &&
19 @HYPHY_INVOCATION@ \$HYPHY_LIB/TemplateBatchFiles/SelectionAnalyses/SLAC.bf > '$slac_log'
20 ]]>
21 </command>
22 <inputs>
23 <expand macro="inputs" />
24 <expand macro="gencode" />
25 <expand macro="branches" />
26 <param name="p_value" type="float" value=".1" min="0" max="1" label="P-value" />
27 <param name="number_of_samples" type="integer" value="100" min="0" max="100000" label="Number of samples used to assess ancestral reconstruction uncertainty" />
28 </inputs>
29 <outputs>
30 <data name="slac_log" format="txt" />
31 <data name="slac_output" format="json" from_work_dir="slac_input.fa.SLAC.json" />
32 </outputs>
33 <tests>
34 <test>
35 <param name="input_file" ftype="fasta" value="absrel-in1.fa" />
36 <param name="input_nhx" ftype="nhx" value="absrel-in1.nhx" />
37 <output name="slac_output" file="slac-out1.json" compare="sim_size" />
38 </test>
39 </tests>
40 <help>
41 <![CDATA[
42 SLAC (Single-Likelihood Ancestor Counting) uses a combination of maximum-likelihood and counting approaches to infer nonsynonymous and synonymous substitution rates on a per-site basis for a given coding alignment and corresponding phylogeny. SLAC assumes that the selection pressure for each site is constant along the entire phylogeny.
43 ]]>
44 </help>
45 <expand macro="citations">
46 <citation type="doi">10.1093/molbev/msi105</citation>
47 </expand>
48 </tool>