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annotate orthologs/ucsb_hamster/translate.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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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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1 <tool id="translate" name="Translate">
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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2 <description>Runs Translate</description>
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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3 <command interpreter="perl">translate.pl -infile=$inFile 2&gt;log.txt</command>
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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4 <inputs>
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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5 <param name="inFile" type="data" format="fasta" label="fasta file" />
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6
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7 </inputs>
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8
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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9 <outputs>
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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10 <data format="fasta" label="Translated" from_work_dir="translate_tc.out" />
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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11 </outputs>
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12
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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13 <help>
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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14 Translate is a part of Hamster.
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15
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16 Note: Translate will only read the first 20 characters of a header. If there are identical
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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17 headers within your file, the script will crash.
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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18
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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19 Input: FASTA file containing ESTs.
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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20
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21 </help>
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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22 </tool>
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