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annotate alignment/phytab_muscle.xml @ 0:5b9a38ec4a39 draft default tip
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author | osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> |
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date | Tue, 11 Mar 2014 12:19:13 -0700 |
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1 <tool id="phytab_muscle" name="phytab MUSCLE" version="1.0"> |
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2 <description>MUSCLE: Multiple sequence alignment. Input can be FASTA or phytab format.</description> |
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3 <requirements> |
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4 <requirement type="package">muscle</requirement> |
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5 </requirements> |
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6 <command interpreter="python"> |
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7 phytab_muscle.py -i $data > $muscle_stdout 2>&1 |
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8 </command> |
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9 <inputs> |
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10 <param format="txt" name="data" type="data" label="Sequence data" help="This should be sequence data in fasta or phytab format"/> |
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11 </inputs> |
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12 <outputs> |
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13 <data format="txt" name="muscle_stdout" label="${tool.name} on ${on_string}: stdout" /> |
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14 <data format="tabular" name="muscle_results" label="${tool.name} on ${on_string}: results" from_work_dir="data/results.data" /> |
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15 </outputs> |
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16 <tests> |
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17 </tests> |
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18 <help> |
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19 **What it does** |
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20 |
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21 Uses MUSCLE to perform multiple sequence alignment on multiple gene families in parallel. |
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22 |
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23 ------ |
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24 |
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25 **Inputs** |
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26 |
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27 Can take as input fasta or phytab format. Phytab allows alignment in parallel of multiple separate gene families/paralogs. See: |
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28 http://osiris-phylogenetics.blogspot.com/2012/09/introduction-to-phytab-format.html |
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29 |
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30 ------ |
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31 |
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32 **Outputs** |
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33 |
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34 Either a fasta file or phytab file of aligned sequences |
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35 |
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36 ------- |
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37 |
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38 **Additional Information** |
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39 |
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40 Please direct questions or comments to ucsb_phylogenetics@lifesci.ucsb.edu or, if you can, enter them on the osiris_phylogenetics site at bitbucket.org |
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41 |
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42 ------- |
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43 |
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44 **Citations** |
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45 |
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46 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 citing the following. |
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47 |
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48 Current Osiris Citation is here |
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49 |
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50 http://osiris-phylogenetics.blogspot.com/2012/10/citation.html |
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51 |
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52 Additional Citations for this tool |
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53 |
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54 Runs MUSCLE 3.8 Multiple Sequence Alignment |
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55 See MUSCLE help: http://www.drive5.com/muscle/muscle_userguide3.8.html |
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56 |
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57 </help> |
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58 </tool> |
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59 |
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60 |