Mercurial > repos > rdvelazquez > hyphy_relax

annotate hyphy_relax.xml @ 3:0648b03f1d2f draft

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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
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1 <?xml version="1.0"?>
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2 <tool id="hyphy_relax" name="HyPhy-RELAX" version="@VERSION@+galaxy0">
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3 <description>Detect relaxed selection in a codon-based phylogenetic framework</description>
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="requirements" />
3
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8 <expand macro="version_command" />
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9 <command detect_errors="exit_code">
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10 <![CDATA[
3
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11 #if $treeAnnotations == 2:
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12 ln -s '$input_file' relax_input.fa &&
a9f460ad3ffe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'17327d46ff082448f0a0fc3b6827f5d9d6124a10\n'-dirty
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13 ln -s '$input_nhx' relax_input.nhx &&
a9f460ad3ffe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'17327d46ff082448f0a0fc3b6827f5d9d6124a10\n'-dirty
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14 echo $gencodeid > tool_params &&
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15 echo `pwd`/relax_input.fa >> tool_params &&
a9f460ad3ffe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'17327d46ff082448f0a0fc3b6827f5d9d6124a10\n'-dirty
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16 echo `pwd`/relax_input.nhx >> tool_params &&
3
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17 echo '$treeAnnotations' >> tool_params &&
0648b03f1d2f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'66899249856184fad03efcca5d444084d78eac83\n'-dirty
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18 echo '3' &&
2
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19 echo '2' &&
3
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20 echo '$analysisType' >> tool_params &&
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21 @HYPHY_INVOCATION@ \$HYPHY_LIB/TemplateBatchFiles/SelectionAnalyses/RELAX.bf > '$relax_log'
3
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22 #else:
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23 ln -s '$input_file' relax_input.fa &&
0648b03f1d2f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'66899249856184fad03efcca5d444084d78eac83\n'-dirty
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24 ln -s '$input_nhx' relax_input.nhx &&
0648b03f1d2f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'66899249856184fad03efcca5d444084d78eac83\n'-dirty
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25 echo $gencodeid > tool_params &&
0648b03f1d2f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'66899249856184fad03efcca5d444084d78eac83\n'-dirty
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26 echo `pwd`/relax_input.fa >> tool_params &&
0648b03f1d2f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'66899249856184fad03efcca5d444084d78eac83\n'-dirty
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27 echo `pwd`/relax_input.nhx >> tool_params &&
0648b03f1d2f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'66899249856184fad03efcca5d444084d78eac83\n'-dirty
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28 echo '$treeAnnotations' >> tool_params &&
0648b03f1d2f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'66899249856184fad03efcca5d444084d78eac83\n'-dirty
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29 echo '2' &&
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30 echo '$analysisType' >> tool_params &&
0648b03f1d2f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'66899249856184fad03efcca5d444084d78eac83\n'-dirty
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31 @HYPHY_INVOCATION@ \$HYPHY_LIB/TemplateBatchFiles/SelectionAnalyses/RELAX.bf > '$relax_log'
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32 #end if
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33 ]]>
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34 </command>
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35 <inputs>
3
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36 <expand macro="inputs" />
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37 <expand macro="gencode" />
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38 <param name="analysisType" type="select" label="Analysis Type">
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39 <option value="1">All</option>
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40 <option value="2">Minimal</option>
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41 </param>
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42 <param name="treeAnnotations" type="select" label="Tree Annotations">
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43 <option value="1">TEST only</option>
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44 <option value="2">TEST and REFERENCE</option>
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45 </param>
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46 </inputs>
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47 <outputs>
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48 <data name="relax_log" format="txt" />
3
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49 <data name="relax_output" format="hyphy_json_results" from_work_dir="relax_input.fa.RELAX.json" />
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50 </outputs>
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51 <tests>
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52 <test>
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53 <param name="input_file" ftype="fasta" value="relax-in1.fa" />
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54 <param name="input_nhx" ftype="nhx" value="relax-in1.nhx" />
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55 <output name="relax_output" file="relax-out1.json" compare="sim_size" />
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56 </test>
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57 </tests>
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58 <help>
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59 <![CDATA[
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60 RELAX (Detect relaxed selection in a codon-based phylogenetic framework)
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61 ]]>
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62 </help>
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63 <expand macro="citations">
3
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64 <citation type="doi">10.1093/molbev/msu400</citation>
0
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65 </expand>
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66 </tool>