Mercurial > repos > rdvelazquez > hyphy_relax
diff hyphy_relax.xml @ 3:0648b03f1d2f draft
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 |
line wrap: on
line diff
--- a/hyphy_relax.xml Tue Jan 08 11:34:44 2019 -0500 +++ b/hyphy_relax.xml Mon Feb 11 20:18:43 2019 -0500 @@ -5,48 +5,36 @@ <import>macros.xml</import> </macros> <expand macro="requirements" /> - <version_command>HYPHYMP --version | tail -n 1 | awk '{print $1}'</version_command> + <expand macro="version_command" /> <command detect_errors="exit_code"> <![CDATA[ - #if $treeAnnotations == 2: - ln -s '$input_file' relax_input.fa && - ln -s '$input_nhx' relax_input.nhx && - echo $gencodeid > tool_params && - echo `pwd`/relax_input.fa >> tool_params && - echo `pwd`/relax_input.nhx >> tool_params && - echo '3' && - echo '2' && - echo '$analysisType' >> tool_params && - @HYPHY_INVOCATION@ \$HYPHY_LIB/TemplateBatchFiles/SelectionAnalyses/RELAX.bf > '$relax_log' - #else: + #if $treeAnnotations == 2: ln -s '$input_file' relax_input.fa && ln -s '$input_nhx' relax_input.nhx && echo $gencodeid > tool_params && echo `pwd`/relax_input.fa >> tool_params && echo `pwd`/relax_input.nhx >> tool_params && + echo '$treeAnnotations' >> tool_params && + echo '3' && echo '2' && - echo '$analysisType' > tool_params && + echo '$analysisType' >> tool_params && @HYPHY_INVOCATION@ \$HYPHY_LIB/TemplateBatchFiles/SelectionAnalyses/RELAX.bf > '$relax_log' - #end if + #else: + ln -s '$input_file' relax_input.fa && + ln -s '$input_nhx' relax_input.nhx && + echo $gencodeid > tool_params && + echo `pwd`/relax_input.fa >> tool_params && + echo `pwd`/relax_input.nhx >> tool_params && + echo '$treeAnnotations' >> tool_params && + echo '2' && + echo '$analysisType' >> tool_params && + @HYPHY_INVOCATION@ \$HYPHY_LIB/TemplateBatchFiles/SelectionAnalyses/RELAX.bf > '$relax_log' + #end if ]]> </command> <inputs> - <param name="input_file" type="data" format="fasta" label="Input FASTA file" /> - <param name="input_nhx" type="data" format="nhx" label="Input newick file" /> - <param name="gencodeid" type="select" label="Genetic code"> - <option value="1">Universal code</option> - <option value="2">Vertebrate mitochondrial DNA code</option> - <option value="3">Yeast mitochondrial DNA code</option> - <option value="4">Mold, Protozoan and Coelenterate mt; Mycloplasma/Spiroplasma</option> - <option value="5">Invertebrate mitochondrial DNA code</option> - <option value="6">Ciliate, Dasycladacean and Hexamita Nuclear code</option> - <option value="7">Echinoderm mitochondrial DNA code</option> - <option value="8">Euplotid Nuclear code</option> - <option value="9">Alternative Yeast Nuclear code</option> - <option value="10">Ascidian mitochondrial DNA code</option> - <option value="11">Flatworm mitochondrial DNA code</option> - <option value="12">Blepharisma Nuclear code</option> - </param> + <expand macro="inputs" /> + <expand macro="gencode" /> <param name="analysisType" type="select" label="Analysis Type"> <option value="1">All</option> <option value="2">Minimal</option> @@ -58,7 +46,7 @@ </inputs> <outputs> <data name="relax_log" format="txt" /> - <data name="relax_output" format="json" from_work_dir="relax_input.fa.RELAX.json" /> + <data name="relax_output" format="hyphy_json_results" from_work_dir="relax_input.fa.RELAX.json" /> </outputs> <tests> <test> @@ -73,6 +61,6 @@ ]]> </help> <expand macro="citations"> - <citation type="doi">10.1093/molbev/msv022</citation> + <citation type="doi">10.1093/molbev/msu400</citation> </expand> </tool>