Mercurial > repos > rdvelazquez > hyphy_fade

comparison hyphy_fade.xml @ 7:a7305e34418f draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'446f1cfedd192ab0e7456495383c2099331379cc\n'-dirty
author rdvelazquez
date Mon, 11 Feb 2019 14:12:14 -0500
parents e445c2dc2cce
children 4377e155b9d1
comparison
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6:e445c2dc2cce 7:a7305e34418f
36 echo '$concentration' >> tool_params && 36 echo '$concentration' >> tool_params &&
37 @HYPHY_INVOCATION@ \$HYPHY_LIB/TemplateBatchFiles/SelectionAnalyses/FADE.bf > '$fade_log' 37 @HYPHY_INVOCATION@ \$HYPHY_LIB/TemplateBatchFiles/SelectionAnalyses/FADE.bf > '$fade_log'
38 #end if 38 #end if
39 ]]></command> 39 ]]></command>
40 <inputs> 40 <inputs>
41 <param name="input_file" type="data" format="fasta" label="Input FASTA file"/> 41 <param name="input_file" type="data" format="fasta" label="Input amino acid FASTA file"/>
42 <param name="input_nhx" type="data" format="nhx" label="Input newick file"/> 42 <param name="input_nhx" type="data" format="nhx" label="Input rooted newick file"/>
43 <param name="branches" type="select" label="Set of branches to test"> 43 <param name="branches" type="select" label="Set of branches to test">
44 <option value="1">All branches</option> 44 <option value="1">All branches</option>
45 <option value="2">Internal branches</option> 45 <option value="2">Internal branches</option>
46 <option value="3">Leaf branches</option> 46 <option value="3">Leaf branches</option>
47 <option value="4">Unlabeled branches</option> 47 <option value="4">Unlabeled branches</option>
96 Bayes approximations (fastest, recommended default)</option> 96 Bayes approximations (fastest, recommended default)</option>
97 </param> 97 </param>
98 </inputs> 98 </inputs>
99 <outputs> 99 <outputs>
100 <data name="fade_log" format="txt"/> 100 <data name="fade_log" format="txt"/>
101 <data name="fade_output" format="json" from_work_dir="fade_input.fa.FADE.json"/> 101 <data name="fade_output" format="hyphy_json_results" from_work_dir="fade_input.fa.FADE.json"/>
102 </outputs> 102 </outputs>
103 <tests> 103 <tests>
104 <test> 104 <test>
105 <param name="input_file" ftype="fasta" value="fade-in1.fa"/> 105 <param name="input_file" ftype="fasta" value="fade-in1.fa"/>
106 <param name="input_nhx" ftype="nhx" value="fade-in1.nhx"/> 106 <param name="input_nhx" ftype="nhx" value="fade-in1.nhx"/>