Mercurial > repos > ucsb-phylogenetics > osiris_phylogenetics
comparison phyloconversion/remove_phytab_dupes.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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| -1:000000000000 | 0:5b9a38ec4a39 |
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| 1 <tool id="remove_phytab_dupes" name="remove_phytab_dupes" version="1.0"> | |
| 2 <description> Finds duplicates in phytab format files </description> | |
| 3 <command interpreter="perl"> | |
| 4 remove_phytab_dupes.pl $infile $keeplongest $ignoregaps $okfile $dupefile | |
| 5 </command> | |
| 6 <inputs> | |
| 7 <param format="tabular" name="infile" type="data" label="Phytab Input file" help=""/> | |
| 8 <param name="keeplongest" type="select" optional="false" label="Keep which duplicate?"> | |
| 9 <option value="1">Keep Longest Duplicate</option> | |
| 10 <option value="0">Keep First Duplicate in File</option> | |
| 11 </param> | |
| 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.'/> | |
| 13 </inputs> | |
| 14 <outputs> | |
| 15 <data format="tabular" name="okfile" label="Unique phytab lines from ${on_string}" /> | |
| 16 <data format="tabular" name="dupefile" label="Duplicated phytab lines from ${on_string}" /> | |
| 17 </outputs> | |
| 18 <help> | |
| 19 **What it does** | |
| 20 | |
| 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. | |
| 22 | |
| 23 ------ | |
| 24 | |
| 25 **Inputs** | |
| 26 | |
| 27 1. PHYTAB format input file. | |
| 28 2. Choose whether to keep the longest or first sequence of a duplicated species in output file one. | |
| 29 3. Choose whether to ignore gap characters (-) when comparing length of sequences for input #2. | |
| 30 | |
| 31 ------ | |
| 32 | |
| 33 **Outputs** | |
| 34 | |
| 35 Two PHYTAB format files. One contains only unique species. The other contains duplicates. | |
| 36 | |
| 37 ------- | |
| 38 | |
| 39 **Citations** | |
| 40 | |
| 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. | |
| 42 | |
| 43 Current Osiris Citation is here | |
| 44 | |
| 45 http://osiris-phylogenetics.blogspot.com/2012/10/citation.html | |
| 46 | |
| 47 </help> | |
| 48 </tool> |