Mercurial > repos > ucsb-phylogenetics > osiris_phylogenetics
comparison getdata/genbankstrip.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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| -1:000000000000 | 0:5b9a38ec4a39 |
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| 1 <tool id="genbankstrip" name="GenBank_strip" version="1.0.0"> | |
| 2 <description> Extracts sequences from GenBank files by gene name </description> | |
| 3 <command interpreter="perl"> | |
| 4 genbankstrip.pl "-f"$data_file "-g"$gene "-l"$length $sp -op | |
| 5 </command> | |
| 6 <inputs> | |
| 7 <param format="txt" name="data_file" type="data" optional="false" label="GenBank flat file"/> | |
| 8 <param name="gene" type="text" label="Gene to extract" help="Name must match the GenBank files or be synonymized" /> | |
| 9 <param name="length" type="integer" value="75" label="Minimum gene length" help="Does not retain short genes." /> | |
| 10 <param name='sp' type='boolean' checked='true' truevalue='-s' falsevalue='' label='Ignore undefined species' help='For example Vargula sp. would be ignored' /> | |
| 11 </inputs> | |
| 12 <outputs> | |
| 13 <data format="tabular" name="stripfile" label="Summary ${tool.name} with ${on_string}" from_work_dir="striplist.txt"/> | |
| 14 <data format="tabular" name="phytabfile" label="Phytab Data ${tool.name} with ${on_string}" from_work_dir="osiris_gbs.phytab"/> | |
| 15 </outputs> | |
| 16 <help> | |
| 17 **What it does** | |
| 18 | |
| 19 Extracts sequences from GenBank flat file based on gene name. | |
| 20 | |
| 21 ------ | |
| 22 | |
| 23 **Inputs** | |
| 24 | |
| 25 There are two alternative ways to input information. | |
| 26 1. A list of Accession numbers in a text file that is uploaded to the Galaxy history. | |
| 27 2. Optionally, the user can paste in a list of accession numbers separated by spaces. | |
| 28 | |
| 29 ------ | |
| 30 | |
| 31 **Outputs** | |
| 32 | |
| 33 The user selects which output format to use for data downloaded from GenBank. Options Include:: | |
| 34 1. GenBank format | |
| 35 2. FASTA format | |
| 36 3. phytab format | |
| 37 | |
| 38 phytab format includes a gene name, which is not standardized in GenBank format, so the user must add manually the gene | |
| 39 family names for all entries. If adding only one gene name, that will be used for all entries. | |
| 40 | |
| 41 ------- | |
| 42 | |
| 43 **Additional Information** | |
| 44 | |
| 45 phytab format is described here: | |
| 46 http://osiris-phylogenetics.blogspot.com/2012/09/introduction-to-phytab-format.html | |
| 47 | |
| 48 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 | |
| 49 | |
| 50 ------- | |
| 51 | |
| 52 **Citations** | |
| 53 | |
| 54 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. | |
| 55 | |
| 56 Current Osiris Citation is here | |
| 57 | |
| 58 http://osiris-phylogenetics.blogspot.com/2012/10/citation.html | |
| 59 | |
| 60 </help> | |
| 61 </tool> | |
| 62 | |
| 63 | |
| 64 | |
| 65 |