Mercurial > repos > rdvelazquez > hyphy_gard

comparison macros.xml @ 5:9640a5b51502 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6c73b2e4c05bdddaef2026feb1073c1b0b4aa12e-dirty
author rdvelazquez
date Fri, 07 Jun 2019 10:20:19 -0400
parents 9e533457ebc0
children
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4:876a69d2c6d7 5:9640a5b51502
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="Universal">Universal code</option>
10 <option value="2">Vertebrate mitochondrial DNA code</option> 10 <option value="Vertebrate-mtDNA">Vertebrate mitochondrial DNA code</option>
11 <option value="3">Yeast mitochondrial DNA code</option> 11 <option value="Yeast-mtDNA">Yeast mitochondrial DNA code</option>
12 <option value="4">Mold, Protozoan and Coelenterate mt; Mycloplasma/Spiroplasma</option> 12 <option value="Mold-Protozoan-mtDNA">Mold, Protozoan and Coelenterate mt; Mycloplasma/Spiroplasma</option>
13 <option value="5">Invertebrate mitochondrial DNA code</option> 13 <option value="Invertebrate-mtDNA">Invertebrate mitochondrial DNA code</option>
14 <option value="6">Ciliate, Dasycladacean and Hexamita Nuclear code</option> 14 <option value="Ciliate-Nuclear">Ciliate, Dasycladacean and Hexamita Nuclear code</option>
15 <option value="7">Echinoderm mitochondrial DNA code</option> 15 <option value="Echinoderm-mtDNA">Echinoderm mitochondrial DNA code</option>
16 <option value="8">Euplotid Nuclear code</option> 16 <option value="Euplotid-Nuclear">Euplotid Nuclear code</option>
17 <option value="9">Alternative Yeast Nuclear code</option> 17 <option value="Alt-Yeast-Nuclear">Alternative Yeast Nuclear code</option>
18 <option value="10">Ascidian mitochondrial DNA code</option> 18 <option value="Ascidian-mtDNA">Ascidian mitochondrial DNA code</option>
19 <option value="11">Flatworm mitochondrial DNA code</option> 19 <option value="Flatworm-mtDNA,">Flatworm mitochondrial DNA code</option>
20 <option value="12">Blepharisma Nuclear code</option> 20 <option value="Blepharisma-Nuclear">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="All">All branches</option>
26 <option value="2">Internal branches</option> 26 <option value="Internal">Internal branches</option>
27 <option value="3">Leaf branches</option> 27 <option value="Leaves">Leaf branches</option>
28 <option value="4">Unlabeled branches</option> 28 <option value="'Unlabeled-branches'">Unlabeled branches</option>
29 </param> 29 </param>
30 </xml>
31 <xml name="version_command">
32 <version_command>HYPHYMP --version | tail -n 1 | awk '{print $1}'</version_command>
33 </xml> 30 </xml>
34 <xml name="citations"> 31 <xml name="citations">
35 <citations> 32 <citations>
36 <citation type="doi">10.1093/bioinformatics/bti079</citation> 33 <citation type="doi">10.1093/bioinformatics/bti079</citation>
37 <yield/> 34 <yield/>
38 </citations> 35 </citations>
39 </xml> 36 </xml>
40 <token name="@VERSION@">2.3.14</token> 37 <token name="@VERSION@">2.5.0</token>
41 <xml name="requirements"> 38 <xml name="requirements">
42 <requirements> 39 <requirements>
43 <requirement type="package" version="@VERSION@">hyphy</requirement> 40 <requirement type="package" version="@VERSION@">hyphy</requirement>
44 <yield/> 41 <yield/>
45 </requirements> 42 </requirements>
46 </xml> 43 </xml>
47 <token name="@HYPHY_ENVIRONMENT@"><![CDATA[export HYPHY=`which HYPHYMP` && 44 <token name="@HYPHY_ENVIRONMENT@"><![CDATA[export HYPHY=`which hyphy` &&
48 export HYPHY_PATH=`dirname \$HYPHY` && 45 export HYPHY_PATH=`dirname \$HYPHY` &&
49 export HYPHY_LIB=`readlink -f \$HYPHY_PATH/../lib/hyphy` &&]]></token> 46 export HYPHY_LIB=`readlink -f \$HYPHY_PATH/../lib/hyphy` &&]]></token>
50 <token name="@HYPHY_INVOCATION@"><![CDATA[@HYPHY_ENVIRONMENT@ cat tool_params | HYPHYMP LIBPATH=\$HYPHY_LIB ]]></token> 47 <token name="@HYPHY_INVOCATION@"><![CDATA[@HYPHY_ENVIRONMENT@ cat tool_params | hyphy LIBPATH=\$HYPHY_LIB ]]></token>
51 <token name="@HYPHYMPI_INVOCATION@"><![CDATA[export HYPHYMPI=`which HYPHYMPI` &&
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>
55 </macros> 48 </macros>