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comparison hyphy_relax.xml @ 3:0648b03f1d2f draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'66899249856184fad03efcca5d444084d78eac83\n'-dirty
author rdvelazquez
date Mon, 11 Feb 2019 20:18:43 -0500
parents f078fc88982d
children 7782bb7bc7b7
comparison
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2:f078fc88982d 3:0648b03f1d2f
3 <description>Detect relaxed selection in a codon-based phylogenetic framework</description> 3 <description>Detect relaxed selection in a codon-based phylogenetic framework</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 <version_command>HYPHYMP --version | tail -n 1 | awk '{print $1}'</version_command> 8 <expand macro="version_command" />
9 <command detect_errors="exit_code"> 9 <command detect_errors="exit_code">
10 <![CDATA[ 10 <![CDATA[
11 #if $treeAnnotations == 2: 11 #if $treeAnnotations == 2:
12 ln -s '$input_file' relax_input.fa && 12 ln -s '$input_file' relax_input.fa &&
13 ln -s '$input_nhx' relax_input.nhx && 13 ln -s '$input_nhx' relax_input.nhx &&
14 echo $gencodeid > tool_params && 14 echo $gencodeid > tool_params &&
15 echo `pwd`/relax_input.fa >> tool_params && 15 echo `pwd`/relax_input.fa >> tool_params &&
16 echo `pwd`/relax_input.nhx >> tool_params && 16 echo `pwd`/relax_input.nhx >> tool_params &&
17 echo '$treeAnnotations' >> tool_params &&
17 echo '3' && 18 echo '3' &&
18 echo '2' && 19 echo '2' &&
19 echo '$analysisType' >> tool_params && 20 echo '$analysisType' >> tool_params &&
20 @HYPHY_INVOCATION@ \$HYPHY_LIB/TemplateBatchFiles/SelectionAnalyses/RELAX.bf > '$relax_log' 21 @HYPHY_INVOCATION@ \$HYPHY_LIB/TemplateBatchFiles/SelectionAnalyses/RELAX.bf > '$relax_log'
21 #else: 22 #else:
22 ln -s '$input_file' relax_input.fa && 23 ln -s '$input_file' relax_input.fa &&
23 ln -s '$input_nhx' relax_input.nhx && 24 ln -s '$input_nhx' relax_input.nhx &&
24 echo $gencodeid > tool_params && 25 echo $gencodeid > tool_params &&
25 echo `pwd`/relax_input.fa >> tool_params && 26 echo `pwd`/relax_input.fa >> tool_params &&
26 echo `pwd`/relax_input.nhx >> tool_params && 27 echo `pwd`/relax_input.nhx >> tool_params &&
28 echo '$treeAnnotations' >> tool_params &&
27 echo '2' && 29 echo '2' &&
28 echo '$analysisType' > tool_params && 30 echo '$analysisType' >> tool_params &&
29 @HYPHY_INVOCATION@ \$HYPHY_LIB/TemplateBatchFiles/SelectionAnalyses/RELAX.bf > '$relax_log' 31 @HYPHY_INVOCATION@ \$HYPHY_LIB/TemplateBatchFiles/SelectionAnalyses/RELAX.bf > '$relax_log'
30 #end if 32 #end if
31 ]]> 33 ]]>
32 </command> 34 </command>
33 <inputs> 35 <inputs>
34 <param name="input_file" type="data" format="fasta" label="Input FASTA file" /> 36 <expand macro="inputs" />
35 <param name="input_nhx" type="data" format="nhx" label="Input newick file" /> 37 <expand macro="gencode" />
36 <param name="gencodeid" type="select" label="Genetic code">
37 <option value="1">Universal code</option>
38 <option value="2">Vertebrate mitochondrial DNA code</option>
39 <option value="3">Yeast mitochondrial DNA code</option>
40 <option value="4">Mold, Protozoan and Coelenterate mt; Mycloplasma/Spiroplasma</option>
41 <option value="5">Invertebrate mitochondrial DNA code</option>
42 <option value="6">Ciliate, Dasycladacean and Hexamita Nuclear code</option>
43 <option value="7">Echinoderm mitochondrial DNA code</option>
44 <option value="8">Euplotid Nuclear code</option>
45 <option value="9">Alternative Yeast Nuclear code</option>
46 <option value="10">Ascidian mitochondrial DNA code</option>
47 <option value="11">Flatworm mitochondrial DNA code</option>
48 <option value="12">Blepharisma Nuclear code</option>
49 </param>
50 <param name="analysisType" type="select" label="Analysis Type"> 38 <param name="analysisType" type="select" label="Analysis Type">
51 <option value="1">All</option> 39 <option value="1">All</option>
52 <option value="2">Minimal</option> 40 <option value="2">Minimal</option>
53 </param> 41 </param>
54 <param name="treeAnnotations" type="select" label="Tree Annotations"> 42 <param name="treeAnnotations" type="select" label="Tree Annotations">
56 <option value="2">TEST and REFERENCE</option> 44 <option value="2">TEST and REFERENCE</option>
57 </param> 45 </param>
58 </inputs> 46 </inputs>
59 <outputs> 47 <outputs>
60 <data name="relax_log" format="txt" /> 48 <data name="relax_log" format="txt" />
61 <data name="relax_output" format="json" from_work_dir="relax_input.fa.RELAX.json" /> 49 <data name="relax_output" format="hyphy_json_results" from_work_dir="relax_input.fa.RELAX.json" />
62 </outputs> 50 </outputs>
63 <tests> 51 <tests>
64 <test> 52 <test>
65 <param name="input_file" ftype="fasta" value="relax-in1.fa" /> 53 <param name="input_file" ftype="fasta" value="relax-in1.fa" />
66 <param name="input_nhx" ftype="nhx" value="relax-in1.nhx" /> 54 <param name="input_nhx" ftype="nhx" value="relax-in1.nhx" />
71 <![CDATA[ 59 <![CDATA[
72 RELAX (Detect relaxed selection in a codon-based phylogenetic framework) 60 RELAX (Detect relaxed selection in a codon-based phylogenetic framework)
73 ]]> 61 ]]>
74 </help> 62 </help>
75 <expand macro="citations"> 63 <expand macro="citations">
76 <citation type="doi">10.1093/molbev/msv022</citation> 64 <citation type="doi">10.1093/molbev/msu400</citation>
77 </expand> 65 </expand>
78 </tool> 66 </tool>