Mercurial > repos > iuc > hyphy_absrel

comparison hyphy_absrel.xml @ 1:5c87e4907e08 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 12:24:13 -0400
parents 419cd817299c
children de93e1fbdc31
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0:419cd817299c 1:5c87e4907e08
2 <tool id="hyphy_absrel" name="HyPhy-aBSREL" version="@VERSION@+galaxy0"> 2 <tool id="hyphy_absrel" name="HyPhy-aBSREL" version="@VERSION@+galaxy0">
3 <description>adaptive Branch Site Random Effects Likelihood</description> 3 <description>adaptive Branch Site Random Effects Likelihood</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 '$input_file' absrel_input.fa &&
10 <![CDATA[ 10 ln -s '$input_nhx' absrel_input.nhx &&
11 ln -s '$input_file' absrel_input.fa && 11 @HYPHY_INVOCATION@ absrel
12 ln -s '$input_nhx' absrel_input.nhx && 12 --alignment ./absrel_input.fa
13 echo $gencodeid > tool_params && 13 --tree ./absrel_input.nhx
14 echo `pwd`/absrel_input.fa >> tool_params && 14 --code '$gencodeid'
15 echo `pwd`/absrel_input.nhx >> tool_params && 15 --branches '$branches'
16 echo '$branches' >> tool_params && 16 > '$absrel_log'
17 @HYPHY_INVOCATION@ \$HYPHY_LIB/TemplateBatchFiles/SelectionAnalyses/aBSREL.bf 17 ]]></command>
18 #if $log:
19 > '$absrel_log'
20 #end if
21 ]]>
22 </command>
23 <inputs> 18 <inputs>
24 <expand macro="inputs" /> 19 <expand macro="inputs"/>
25 <param name="log" type="boolean" truevalue="" falsevalue="" label="Output aBSREL log to history" /> 20 <param name="log" type="boolean" truevalue="" falsevalue="" label="Output aBSREL log to history"/>
26 <expand macro="gencode" /> 21 <expand macro="gencode"/>
27 <expand macro="branches" /> 22 <expand macro="branches"/>
28 </inputs> 23 </inputs>
29 <outputs> 24 <outputs>
30 <data name="absrel_log" format="txt"> 25 <data name="absrel_log" format="txt">
31 <filter>log</filter> 26 <filter>log</filter>
32 </data> 27 </data>
33 <data name="absrel_output" format="json" from_work_dir="absrel_input.fa.ABSREL.json" /> 28 <data name="absrel_output" format="hyphy_results.json" from_work_dir="absrel_input.fa.ABSREL.json"/>
34 </outputs> 29 </outputs>
35 <tests> 30 <tests>
36 <test> 31 <test>
37 <param name="input_file" ftype="fasta" value="absrel-in1.fa" /> 32 <param name="input_file" ftype="fasta" value="absrel-in1.fa"/>
38 <param name="input_nhx" ftype="nhx" value="absrel-in1.nhx" /> 33 <param name="input_nhx" ftype="nhx" value="absrel-in1.nhx"/>
39 <param name="log" value="false" /> 34 <param name="log" value="false"/>
40 <output name="absrel_output" file="absrel-out1.json" compare="sim_size" /> 35 <output name="absrel_output" file="absrel-out1.json" compare="sim_size"/>
41 </test> 36 </test>
42 </tests> 37 </tests>
43 <help> 38 <help><![CDATA[
44 <![CDATA[
45 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. 39 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.
46 ]]> 40 ]]></help>
47 </help>
48 <expand macro="citations"> 41 <expand macro="citations">
49 <citation type="doi">10.1093/molbev/msv022</citation> 42 <citation type="doi">10.1093/molbev/msv022</citation>
50 </expand> 43 </expand>
51 </tool> 44 </tool>