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comparison mafft.xml @ 5:15974dd17515 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit fc3727b1b39cd5654a523d03e0df2b9ac87ddcda
author rnateam
date Tue, 20 Sep 2016 09:30:47 -0400
parents f0606dfd5195
children aaefa93c2dd2
comparison
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4:f0606dfd5195 5:15974dd17515
14 </version_command> 14 </version_command>
15 <command> 15 <command>
16 <![CDATA[ 16 <![CDATA[
17 #if $cond_flavour.flavourType != 'custom' 17 #if $cond_flavour.flavourType != 'custom'
18 $cond_flavour.flavourType 18 $cond_flavour.flavourType
19
20 #elif $cond_flavour.flavourType == 'custom' 19 #elif $cond_flavour.flavourType == 'custom'
21 ### full parameter options 20 ### full parameter options
22 mafft 21 mafft
23 $cond_flavour.distance_method 22 $cond_flavour.distance_method
24 --retree $cond_flavour.retree 23 --retree $cond_flavour.retree
25 --maxiterate $cond_flavour.iterations 24 --maxiterate $cond_flavour.iterations
26 #end if 25 #end if
27 26
28 ## specify threads to use 27 ## specify threads to use
29 --thread \${GALAXY_SLOTS:-1} 28 --thread \${GALAXY_SLOTS:-1}
30 29
31 $datatype 30 $datatype
32 --ep $ep 31 --ep $ep
33 --op $op 32 --op $op
34 $adjustdirection 33 $adjustdirection
35 34
36 #if $matrix_condition.matrix == "BLOSUM" 35 #if $matrix_condition.matrix == "BLOSUM"
37 --bl ${matrix_condition.BLOSUM} 36 --bl ${matrix_condition.BLOSUM}
38 #elif $matrix_condition.matrix == "PAM" 37 #elif $matrix_condition.matrix == "PAM"
39 --jtt ${matrix_condition.PAM} 38 --jtt ${matrix_condition.PAM}
40 #end if 39 #end if
41 40
42 $reorder 41 $reorder
43 $getTree 42 $getTree
44 $outputFormat 43 $outputFormat
45 $inputSequences > $outputAlignment; 44 $inputSequences > $outputAlignment;
46 45
47 #if $getTree == "--treeout" 46 #if $getTree == "--treeout"
48 mv ${inputSequences}.tree $outputTree; 47 mv ${inputSequences}.tree $outputTree;
49 #end if 48 #end if
50 ]]> 49 ]]>
51 </command> 50 </command>