Mercurial > repos > ucsb-phylogenetics > osiris_phylogenetics
diff phyloconversion/remove_gbs_dupes.xml @ 0:5b9a38ec4a39 draft default tip
First commit of old repositories
| author | osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> |
|---|---|
| date | Tue, 11 Mar 2014 12:19:13 -0700 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/phyloconversion/remove_gbs_dupes.xml Tue Mar 11 12:19:13 2014 -0700 @@ -0,0 +1,44 @@ +<tool id="remove_gbs_dupes" name="remove_gbs_dupes" version="1.0"> + <description> Finds duplicates in genbankstrip output files </description> + <command interpreter="perl"> + remove_gbs_dupes.pl $infile $okfile $dupefile $subsp $var + </command> + <inputs> + <param format="tabular" name="infile" type="data" label="Phytab Input file" help="Output of genbankstrip"/> + <param format="tabular" name="infile" type="data" label="Phytab Input file" help="Output of genbankstrip"/> + <param name='subsp' type='boolean' checked='false' truevalue='1' falsevalue='0' label='Remove lines containing subsp'/> + <param name='var' type='boolean' checked='false' truevalue='1' falsevalue='0' label='Remove lines containing _var_'/> + </inputs> + <outputs> + <data format="tabular" name="okfile" label="Unique phytab lines from ${on_string}" /> + <data format="tabular" name="dupefile" label="Duplicated phytab lines from ${on_string}" /> + </outputs> + <help> +**What it does** + +Finds species names that end in _2 or _3 or ... _N which are duplicate genes in a species in genbankstrip, and it writes those lines to another file. + +------ + +**Inputs** + +1. PHYTAB format input file. + +------ + +**Outputs** + +Two PHYTAB format files. One contains only unique species. The other contains duplicates. + +------- + +**Citations** + +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. + +Current Osiris Citation is here + +http://osiris-phylogenetics.blogspot.com/2012/10/citation.html + + </help> +</tool>