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annotate alignment/phytab_aliscorecut.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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1 <tool id="phytab_aliscorecut" name="phytab AliccoreCut" version="1.0">
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2 <description>Runs Aliscore then Alicut on an aligned sequence in phytab format.</description>
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3 <requirements>
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4 <requirement type="package">aliscore and alicut</requirement>
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5 </requirements>
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6 <command interpreter="python">
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7 aliscorecut.py -i $sequence > $aliscorecut_stdout 2>&amp;1
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8 </command>
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9 <inputs>
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10 <param format="txt" name="sequence" type="data" label="Aligned sequence" help="This should be an aligned sqeuence from UCSB Muscle."/>
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11 </inputs>
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12 <outputs>
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13 <data format="txt" name="aliscorecut_stdout" label="${tool.name} on ${on_string}: stdout" />
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14 <data format="tabular" name="aliscorecut_results" label="${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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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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19 **What it does**
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20
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21 Aliscore identifies ambiguously aligned regions of a multiple sequence alignment. Alicut deletes sites marked by aliscore. This tool combines both into one tool.
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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 Aligned sequences in phytab format
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28
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29 ------
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30
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31 **Outputs**
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32
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33 phytab format
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34
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35 ------
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36
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37 **Additional information**
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38
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39 For information on phytab format see: http://osiris-phylogenetics.blogspot.com/2012/09/introduction-to-phytab-format.html
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40
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41 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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42 bitbucket.org
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43
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44 ------
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45
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46 **Citations**
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47
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48 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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49 citing the following.
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50
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51 Current Osiris Citation is here
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52
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53 http://osiris-phylogenetics.blogspot.com/2012/10/citation.html
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54
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55 Additional Citations for this tool
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56
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57 Aliscore: Kuck P, Meusemann K, Dambach J, Thormann B, von Reumont BM, et al. (2010) Parametric and non-parametric masking of randomness in sequence alignments can be improved and leads to better
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58 resolved trees. Front Zool 7: 10.
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59 </help>
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60 </tool>