Mercurial > repos > rdvelazquez > hyphy_busted

comparison macros.xml @ 3:d0a3511a8f33 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'6e7f074d80e0f35516e223b76e73f019ad45dd74\n'-dirty
author rdvelazquez
date Mon, 18 Feb 2019 15:14:26 -0500
parents 0d4341fca959
children f8abbbc7e29e
comparison
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2:0d4341fca959 3:d0a3511a8f33
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <macros> 2 <macros>
3 <xml name="inputs"> 3 <xml name="inputs">
4 <param name="input_file" type="data" format="fasta" label="Input FASTA file" /> 4 <param name="input_file" type="data" format="fasta" label="Input FASTA file"/>
5 <param name="input_nhx" type="data" format="nhx" label="Input newick file" /> 5 <param name="input_nhx" type="data" format="nhx" label="Input newick file"/>
6 </xml> 6 </xml>
7 <xml name="gencode"> 7 <xml name="gencode">
8 <param name="gencodeid" type="select" label="Genetic code"> 8 <param name="gencodeid" type="select" label="Genetic code">
9 <option value="1">Universal code</option> 9 <option value="1">Universal code</option>
10 <option value="2">Vertebrate mitochondrial DNA code</option> 10 <option value="2">Vertebrate mitochondrial DNA code</option>
11 <option value="3">Yeast mitochondrial DNA code</option> 11 <option value="3">Yeast mitochondrial DNA code</option>
12 <option value="4">Mold, Protozoan and Coelenterate mt; Mycloplasma/Spiroplasma</option> 12 <option value="4">Mold, Protozoan and Coelenterate mt; Mycloplasma/Spiroplasma</option>
13 <option value="5">Invertebrate mitochondrial DNA code</option> 13 <option value="5">Invertebrate mitochondrial DNA code</option>
14 <option value="6">Ciliate, Dasycladacean and Hexamita Nuclear code</option> 14 <option value="6">Ciliate, Dasycladacean and Hexamita Nuclear code</option>
15 <option value="7">Echinoderm mitochondrial DNA code</option> 15 <option value="7">Echinoderm mitochondrial DNA code</option>
16 <option value="8">Euplotid Nuclear code</option> 16 <option value="8">Euplotid Nuclear code</option>
17 <option value="9">Alternative Yeast Nuclear code</option> 17 <option value="9">Alternative Yeast Nuclear code</option>
18 <option value="10">Ascidian mitochondrial DNA code</option> 18 <option value="10">Ascidian mitochondrial DNA code</option>
19 <option value="11">Flatworm mitochondrial DNA code</option> 19 <option value="11">Flatworm mitochondrial DNA code</option>
20 <option value="12">Blepharisma Nuclear code</option> 20 <option value="12">Blepharisma Nuclear code</option>
21 </param> 21 </param>
22 </xml> 22 </xml>
23 <xml name="branches"> 23 <xml name="branches">
24 <param name="branches" type="select" label="Set of branches to test"> 24 <param name="branches" type="select" label="Set of branches to test">
25 <option value="1">All branches</option> 25 <option value="1">All branches</option>
26 <option value="2">Internal branches</option> 26 <option value="2">Internal branches</option>
27 <option value="3">Leaf branches</option> 27 <option value="3">Leaf branches</option>
28 <option value="4">Unlabeled branches</option> 28 <option value="4">Unlabeled branches</option>
29 </param> 29 </param>
30 </xml> 30 </xml>
31 <xml name="version_command"> 31 <xml name="version_command">
32 <version_command>HYPHYMP --version | tail -n 1 | awk '{print $1}'</version_command> 32 <version_command>HYPHYMP --version | tail -n 1 | awk '{print $1}'</version_command>
33 </xml> 33 </xml>
34 <xml name="citations"> 34 <xml name="citations">
35 <citations> 35 <citations>
36 <citation type="doi">10.1093/bioinformatics/bti079</citation> 36 <citation type="doi">10.1093/bioinformatics/bti079</citation>
37 <yield /> 37 <yield/>
38 </citations> 38 </citations>
39 </xml> 39 </xml>
40 <token name="@VERSION@">2.3.14</token> 40 <token name="@VERSION@">2.3.14</token>
41 <xml name="requirements"> 41 <xml name="requirements">
42 <requirements> 42 <requirements>
43 <requirement type="package" version="@VERSION@">hyphy</requirement> 43 <requirement type="package" version="@VERSION@">hyphy</requirement>
44 <yield /> 44 <yield/>
45 </requirements> 45 </requirements>
46 </xml> 46 </xml>
47 <token name="@HYPHY_ENVIRONMENT@"><![CDATA[export HYPHY=`which HYPHYMP` && 47 <token name="@HYPHY_ENVIRONMENT@"><![CDATA[export HYPHY=`which HYPHYMP` &&
48 export HYPHY_PATH=`dirname \$HYPHY` && 48 export HYPHY_PATH=`dirname \$HYPHY` &&
49 export HYPHY_LIB=`readlink -f \$HYPHY_PATH/../lib/hyphy` &&]]> 49 export HYPHY_LIB=`readlink -f \$HYPHY_PATH/../lib/hyphy` &&]]></token>
50 </token> 50 <token name="@HYPHY_INVOCATION@"><![CDATA[@HYPHY_ENVIRONMENT@ cat tool_params | HYPHYMP LIBPATH=\$HYPHY_LIB ]]></token>
51 <token name="@HYPHY_INVOCATION@"><![CDATA[@HYPHY_ENVIRONMENT@ cat tool_params | HYPHYMP LIBPATH=\$HYPHY_LIB ]]></token> 51 <token name="@HYPHYMPI_INVOCATION@"><![CDATA[export HYPHYMPI=`which HYPHYMPI` &&
52 <token name="@HYPHYMPI_INVOCATION@"><![CDATA[@HYPHY_ENVIRONMENT@ cat tool_params | mpirun -np \${GALAXY_SLOTS:-1} HYPHYMPI LIBPATH=\$HYPHY_LIB ]]></token> 52 export HYPHYMPI_PATH=`dirname \$HYPHYMPI` &&
53 export HYPHYMPI_LIB=`readlink -f \$HYPHYMPI_PATH/../lib/hyphy` &&
54 cat tool_params | mpirun -np \${GALAXY_SLOTS:-2} HYPHYMPI LIBPATH=\$HYPHYMPI_LIB ]]></token>
53 </macros> 55 </macros>