Mercurial > repos > rdvelazquez > hyphy_meme

comparison macros.xml @ 1:cffd8bd6e3ec draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'0a555981fa0582d59012c76c01c466db490831ed\n'-dirty
author rdvelazquez
date Mon, 11 Feb 2019 14:31:06 -0500
parents 1fe6d55b5a9b
children 15591ab0d53a
comparison
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0:1fe6d55b5a9b 1:cffd8bd6e3ec
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <macros> 2 <macros>
3 <xml name="citations"> 3 <xml name="inputs">
4 <citations> 4 <param name="input_file" type="data" format="fasta" label="Input FASTA file" />
5 <citation type="doi">10.1093/bioinformatics/bti079</citation> 5 <param name="input_nhx" type="data" format="nhx" label="Input newick file" />
6 <yield/> 6 </xml>
7 </citations> 7 <xml name="gencode">
8 </xml> 8 <param name="gencodeid" type="select" label="Genetic code">
9 <token name="@VERSION@">2.3.14</token> 9 <option value="1">Universal code</option>
10 <xml name="requirements"> 10 <option value="2">Vertebrate mitochondrial DNA code</option>
11 <requirements> 11 <option value="3">Yeast mitochondrial DNA code</option>
12 <requirement type="package" version="@VERSION@"> 12 <option value="4">Mold, Protozoan and Coelenterate mt; Mycloplasma/Spiroplasma</option>
13 hyphy</requirement> 13 <option value="5">Invertebrate mitochondrial DNA code</option>
14 <yield/> 14 <option value="6">Ciliate, Dasycladacean and Hexamita Nuclear code</option>
15 </requirements> 15 <option value="7">Echinoderm mitochondrial DNA code</option>
16 </xml> 16 <option value="8">Euplotid Nuclear code</option>
17 <token name="@HYPHY_INVOCATION@"><![CDATA[export HYPHY=`which HYPHYMP` && 17 <option value="9">Alternative Yeast Nuclear code</option>
18 <option value="10">Ascidian mitochondrial DNA code</option>
19 <option value="11">Flatworm mitochondrial DNA code</option>
20 <option value="12">Blepharisma Nuclear code</option>
21 </param>
22 </xml>
23 <xml name="branches">
24 <param name="branches" type="select" label="Set of branches to test">
25 <option value="1">All branches</option>
26 <option value="2">Internal branches</option>
27 <option value="3">Leaf branches</option>
28 <option value="4">Unlabeled branches</option>
29 </param>
30 </xml>
31 <xml name="version_command">
32 <version_command>HYPHYMP --version | tail -n 1 | awk '{print $1}'</version_command>
33 </xml>
34 <xml name="citations">
35 <citations>
36 <citation type="doi">10.1093/bioinformatics/bti079</citation>
37 <yield />
38 </citations>
39 </xml>
40 <token name="@VERSION@">2.3.14</token>
41 <xml name="requirements">
42 <requirements>
43 <requirement type="package" version="@VERSION@">hyphy</requirement>
44 <yield />
45 </requirements>
46 </xml>
47 <token name="@HYPHY_ENVIRONMENT@"><![CDATA[export HYPHY=`which HYPHYMP` &&
18 export HYPHY_PATH=`dirname \$HYPHY` && 48 export HYPHY_PATH=`dirname \$HYPHY` &&
19 export HYPHY_LIB=`readlink -f \$HYPHY_PATH/../lib/hyphy` && 49 export HYPHY_LIB=`readlink -f \$HYPHY_PATH/../lib/hyphy` &&]]>
20 cat tool_params | HYPHYMP LIBPATH=\$HYPHY_LIB ]]></token> 50 </token>
21 <token name="@HYPHYMPI_INVOCATION@"><![CDATA[export HYPHYMPI=`which HYPHYMPI` && 51 <token name="@HYPHY_INVOCATION@"><![CDATA[@HYPHY_ENVIRONMENT@ cat tool_params | HYPHYMP LIBPATH=\$HYPHY_LIB ]]></token>
22 export HYPHYMPI_PATH=`dirname \$HYPHYMPI` && 52 <token name="@HYPHYMPI_INVOCATION@"><![CDATA[@HYPHY_ENVIRONMENT@ cat tool_params | mpirun -np \${GALAXY_SLOTS:-1} HYPHYMPI LIBPATH=\$HYPHY_LIB ]]></token>
23 export HYPHYMPI_LIB=`readlink -f \$HYPHYMPI_PATH/../lib/hyphy` &&
24 cat tool_params | mpirun -np \${GALAXY_SLOTS:-1} HYPHYMPI LIBPATH=\$HYPHYMPI_LIB ]]></token>
25 </macros> 53 </macros>