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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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children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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1 <tool id="remove_phytab_dupes" name="remove_phytab_dupes" version="1.0">
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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2 <description> Finds duplicates in phytab format files </description>
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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3 <command interpreter="perl">
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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4 remove_phytab_dupes.pl $infile $keeplongest $ignoregaps $okfile $dupefile
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5 </command>
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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6 <inputs>
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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7 <param format="tabular" name="infile" type="data" label="Phytab Input file" help=""/>
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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8 <param name="keeplongest" type="select" optional="false" label="Keep which duplicate?">
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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9 <option value="1">Keep Longest Duplicate</option>
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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10 <option value="0">Keep First Duplicate in File</option>
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11 </param>
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12 <param name='ignoregaps' type='boolean' checked='true' falsevalue ='0' truevalue='1' label='Ignore Gaps' help='Whether to ignore gaps when calculating length for which duplicate to retain. Gaps not removed from file.'/>
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13 </inputs>
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14 <outputs>
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15 <data format="tabular" name="okfile" label="Unique phytab lines from ${on_string}" />
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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16 <data format="tabular" name="dupefile" label="Duplicated phytab lines from ${on_string}" />
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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17 </outputs>
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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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 Finds lines with identical species (column 1) and partition (column 2) and writes on of the duplicates to one file, unique lines to another file.
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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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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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27 1. PHYTAB format input file.
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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28 2. Choose whether to keep the longest or first sequence of a duplicated species in output file one.
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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29 3. Choose whether to ignore gap characters (-) when comparing length of sequences for input #2.
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30
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31 ------
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32
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33 **Outputs**
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34
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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35 Two PHYTAB format files. One contains only unique species. The other contains duplicates.
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36
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37 -------
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38
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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39 **Citations**
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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40
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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41 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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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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42
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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43 Current Osiris Citation is here
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44
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45 http://osiris-phylogenetics.blogspot.com/2012/10/citation.html
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46
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47 </help>
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48 </tool>