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comparison hyphy_slac.xml @ 1:c2bed8cc8fc1 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
author iuc
date Wed, 21 Aug 2019 12:27:21 -0400
parents 9da003917dcb
children a603e2f909e5
comparison
equal deleted inserted replaced
0:9da003917dcb 1:c2bed8cc8fc1
2 <tool id="hyphy_slac" name="HyPhy-SLAC" version="@VERSION@+galaxy0"> 2 <tool id="hyphy_slac" name="HyPhy-SLAC" version="@VERSION@+galaxy0">
3 <description>Single Likelihood Ancestor Counting</description> 3 <description>Single Likelihood Ancestor Counting</description>
4 <macros> 4 <macros>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
7 <expand macro="requirements" /> 7 <expand macro="requirements"/>
8 <expand macro="version_command" /> 8 <command detect_errors="exit_code"><![CDATA[
9 <command detect_errors="exit_code"> 9 ln -s '$input_file' slac_input.fa &&
10 <![CDATA[ 10 ln -s '$input_nhx' slac_input.nhx &&
11 ln -s '$input_file' slac_input.fa && 11 @HYPHY_INVOCATION@ slac
12 ln -s '$input_nhx' slac_input.nhx && 12 --alignment ./slac_input.fa
13 echo $gencodeid > tool_params && 13 --tree ./slac_input.nhx
14 echo `pwd`/slac_input.fa >> tool_params && 14 --code '$gencodeid'
15 echo `pwd`/slac_input.nhx >> tool_params && 15 --branches '$branches'
16 echo '$branches' >> tool_params && 16 --samples '$number_of_samples'
17 echo '$number_of_samples' >> tool_params && 17 --pvalue '$p_value'
18 echo '$p_value' >> tool_params && 18 > '$slac_log'
19 @HYPHY_INVOCATION@ \$HYPHY_LIB/TemplateBatchFiles/SelectionAnalyses/SLAC.bf > '$slac_log' 19 ]]></command>
20 ]]>
21 </command>
22 <inputs> 20 <inputs>
23 <expand macro="inputs" /> 21 <expand macro="inputs"/>
24 <expand macro="gencode" /> 22 <expand macro="gencode"/>
25 <expand macro="branches" /> 23 <expand macro="branches"/>
26 <param name="p_value" type="float" value=".1" min="0" max="1" label="P-value" /> 24 <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" /> 25 <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> 26 </inputs>
29 <outputs> 27 <outputs>
30 <data name="slac_log" format="txt" /> 28 <data name="slac_log" format="txt"/>
31 <data name="slac_output" format="json" from_work_dir="slac_input.fa.SLAC.json" /> 29 <data name="slac_output" format="hyphy_results.json" from_work_dir="slac_input.fa.SLAC.json"/>
32 </outputs> 30 </outputs>
33 <tests> 31 <tests>
34 <test> 32 <test>
35 <param name="input_file" ftype="fasta" value="absrel-in1.fa" /> 33 <param name="input_file" ftype="fasta" value="absrel-in1.fa"/>
36 <param name="input_nhx" ftype="nhx" value="absrel-in1.nhx" /> 34 <param name="input_nhx" ftype="nhx" value="absrel-in1.nhx"/>
37 <output name="slac_output" file="slac-out1.json" compare="sim_size" /> 35 <output name="slac_output" file="slac-out1.json" compare="sim_size"/>
38 </test> 36 </test>
39 </tests> 37 </tests>
40 <help> 38 <help><![CDATA[
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. 39 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 ]]> 40 ]]></help>
44 </help>
45 <expand macro="citations"> 41 <expand macro="citations">
46 <citation type="doi">10.1093/molbev/msi105</citation> 42 <citation type="doi">10.1093/molbev/msi105</citation>
47 </expand> 43 </expand>
48 </tool> 44 </tool>