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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="gap-rem" name="Sequence Gap Remover" version="1.0">
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2 <description>Removes gap in sequences</description>
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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3 <command interpreter="perl">seqfill.pl $file $question_mark $hyphen $N $usePart $pfile</command>
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4 <inputs>
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5 <param format="phylipnon" name="file" type="data" label="File" />
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6 <param type ="boolean" name="usePart" checked="true" truevalue="true" falsevalue="false" label="Also use Partition File -- if unchecked, it will be ignored." />
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7 <param format="txt" name="pfile" checked="true" type="data" label="Partition file" />
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8 <param type="boolean" name="question_mark" checked="true" truevalue="true" falsevalue="false" label="'?' signifies gap" />
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9 <param type="boolean" name="hyphen" checked="true" truevalue="true" falsevalue="false" label="'-' signifies gap" />
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10 <param type="boolean" name="N" checked="true" truevalue="true" falsevalue="false" label="'N' signifies gap"/>
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11 </inputs>
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12
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13 <outputs>
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14 <data from_work_dir="out.phylipnon" format="phylipnon" name="out1" label="DATA ${tool.name}" />
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15 <data from_work_dir="partOut.txt" format="txt" name="out2" label="PARTITION ${tool.name}" />
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16 </outputs>
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17
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18 <help>
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19 **What it does**
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20 Sequence Gap Remover
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21
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22 Gaps across all species are introduced by phylocatenator when selecting pre-aligned datasets
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23
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24 Takes an input phylip file and removes any specified gap characters that exist in the same columns of containing sequences.
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25
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26 ------
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27
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28 **Inputs**
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29
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30 Phylip
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31
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32 ------
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33
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34 **Outputs**
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35
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36 Text file
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37
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38 ------
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39
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40 **Additional Information**
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41
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42 Please direct questions or comments to ucsb_phylogenetics@lifesci.ucsb.edu or, if you can, enter them on the osiris_phylogenetics site at
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43 bitbucket.org
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44
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45 -------
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46
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47 **Citations**
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48
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49 This tool is part of the Osiris Phylogenetics Tool Package for Galaxy. If you make extensive use of this tool in a publication, please consider
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50 citing the following.
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51
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52 Current Osiris Citation is here
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53
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54 http://osiris-phylogenetics.blogspot.com/2012/10/citation.html
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55 </help>
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56
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57 </tool>