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annotate orthologs/evolmap_output.xml @ 0:5b9a38ec4a39 draft default tip

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author osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
date Tue, 11 Mar 2014 12:19:13 -0700
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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1 <tool id="evolmap_output" name="EvolMAP Output Tool">
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2 <description>Modifies EvolMAP output</description>
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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3 <command interpreter="perl">output.pl $file $numDiffGenes '$speciesList'
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4 #for $file in $fileList
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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5 ${file.treeFile}
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6 #end for</command>
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7
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8 <inputs>
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9 <repeat name="fileList" title="Species fasta files - must be same order as original tree">
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10 <param name="treeFile" type="data" format="fasta" label="fasta file"/>
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11 </repeat>
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12 <param name="file" type="data" label="EvolMAP output file"/>
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13 <param name="numDiffGenes" type="integer" value="1" label="Number of different species" />
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14 <param name="speciesList" type="text" area="true" size="3x25" label="Species tree - Must be same format as original EvolMAP run." />
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15 </inputs>
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16
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17 <outputs>
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18 <data from_work_dir="result.dat" format="txt"/>
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19 </outputs>
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20
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21 <help>
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22
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23 http://labs.eemb.ucsb.edu/oakley/todd/
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24
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25 Modifies EvolMAP output. Must provide the original EvolMAP output and files used.
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26
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27 Input preconditions:
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28 Species fasta files - must be inputted in the same order as the original tree from the EvolMAP run
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29 EvolMAP output file - must be from an EvolMAP run
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30 Number of different species - the number of different species you want searched and pulled to the output file
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31 Species tree - must be the same tree you used to get the EvolMAP output file in the original EvolMAP run
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32
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33 Input file format:
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34 FASTA (.fasta/.fa)
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35
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36 Output format:
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37 Text (txt)
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38 </help>
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39
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40 </tool>