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comparison readseq.xml @ 1:36e5445b7807 draft

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author dereeper
date Tue, 08 Jan 2019 10:14:18 -0500
parents 225031d5c818
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0:225031d5c818 1:36e5445b7807
15 <exit_code range="1:" level="fatal" /> 15 <exit_code range="1:" level="fatal" />
16 </stdio> 16 </stdio>
17 17
18 <!-- [REQUIRED] The command to execute --> 18 <!-- [REQUIRED] The command to execute -->
19 <command> 19 <command>
20 readseq $filein -f $format >> $fileout_log 2>&amp;1 &amp;&amp; 20 java -jar /home/galaxy/data/jars/readseq.jar $filein -f $format >> $fileout_log 2>&amp;1 &amp;&amp;
21 #if str( $format ) == "1": 21 #if str( $format ) == "1":
22 mv ${filein}.ig $fileout 22 mv ${filein}.ig $fileout
23 #elif str( $format ) == "2" : 23 #elif str( $format ) == "2" :
24 mv ${filein}.gb $fileout 24 mv ${filein}.gb $fileout
25 #elif str( $format ) == "3" : 25 #elif str( $format ) == "3" :
33 #elif str( $format ) == "8" : 33 #elif str( $format ) == "8" :
34 mv ${filein}.fasta $fileout 34 mv ${filein}.fasta $fileout
35 #elif str( $format ) == "11" : 35 #elif str( $format ) == "11" :
36 mv ${filein}.phylip2 $fileout 36 mv ${filein}.phylip2 $fileout
37 #elif str( $format ) == "12" : 37 #elif str( $format ) == "12" :
38 mv ${filein}.phylip $fileout 38 perl $__tool_directory__/complete_names.pl ${filein} ${filein}.phylip $fileout
39 #elif str( $format ) == "13" : 39 #elif str( $format ) == "13" :
40 mv ${filein}.seq $fileout 40 mv ${filein}.seq $fileout
41 #elif str( $format ) == "14" : 41 #elif str( $format ) == "14" :
42 mv ${filein}.pir $fileout 42 mv ${filein}.pir $fileout
43 #elif str( $format ) == "15" : 43 #elif str( $format ) == "15" :