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annotate mafft.xml @ 14:6f28e90db932 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit 1570f3a28232b4b88385cdfbb68f79d80ff1dabb
author bgruening
date Tue, 31 Oct 2023 15:48:53 +0000
parents 4de39704d423
children bf28a8cff401
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
rnateam
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1 <?xml version="1.0" encoding="UTF-8"?>
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6f28e90db932 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit 1570f3a28232b4b88385cdfbb68f79d80ff1dabb
bgruening
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2 <tool id="rbc_mafft" name="MAFFT" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
6f28e90db932 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit 1570f3a28232b4b88385cdfbb68f79d80ff1dabb
bgruening
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3 <description>Multiple alignment program for amino acid or nucleotide sequences</description>
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aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
rnateam
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4 <macros>
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
rnateam
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5 <import>macros.xml</import>
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
rnateam
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6 </macros>
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6f28e90db932 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit 1570f3a28232b4b88385cdfbb68f79d80ff1dabb
bgruening
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7 <expand macro="biotools"/>
7
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
rnateam
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8 <expand macro="requirements" />
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
rnateam
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9 <stdio>
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
rnateam
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10 <exit_code range="1:" level="fatal" description="Error occurred. Please check Tool Standard Error" />
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
rnateam
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11 <exit_code range=":-1" level="fatal" description="Error occurred. Please check Tool Standard Error" />
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
rnateam
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12 </stdio>
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
rnateam
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13 <version_command> <![CDATA[
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
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14 mafft --version
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
rnateam
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15 ]]>
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
rnateam
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16 </version_command>
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
rnateam
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17 <command>
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
rnateam
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18 <![CDATA[
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
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19
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
rnateam
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20 #if $cond_flavour.flavourType == 'custom'
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
rnateam
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21 #if $cond_flavour.dist_flavour.distance_method == '--fastapair'
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
rnateam
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22 export FASTA_4_MAFFT=`which fasta36`;
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
rnateam
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23 #end if
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
rnateam
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24 #end if
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
rnateam
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25
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
rnateam
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26 #if $cond_flavour.flavourType != 'custom'
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
rnateam
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27 $cond_flavour.flavourType
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
rnateam
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28 #elif $cond_flavour.flavourType == 'custom'
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
rnateam
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29 ### full parameter options
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
rnateam
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30 mafft
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
rnateam
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31 $cond_flavour.dist_flavour.distance_method
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
rnateam
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32 #if $cond_flavour.dist_flavour.distance_method == '--6merpair'
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
rnateam
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33 --retree $cond_flavour.dist_flavour.retree
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
rnateam
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34 $cond_flavour.dist_flavour.distance_method.usetree.parttree
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
rnateam
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35
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
rnateam
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36 #if $cond_flavour.dist_flavour.distance_method.usetree.parttree==--parttree
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
rnateam
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37 $cond_flavour.dist_flavour.distance_method.usetree.treedistance
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
rnateam
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38 $cond_flavour.dist_flavour.distance_method.usetree.partsize
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
rnateam
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39 $cond_flavour.dist_flavour.distance_method.usetree.groupsize
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
rnateam
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40 #end if
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
rnateam
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41
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
rnateam
parents: 5
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42 #elif $cond_flavour.dist_flavour.distance_method == '--globalpair'
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
rnateam
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43 --weighti $cond_flavour.dist_flavour.weighti
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
rnateam
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44 #elif $cond_flavour.dist_flavour.distance_method == '--localpair'
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
rnateam
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45 --weighti $cond_flavour.dist_flavour.weighti
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
rnateam
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46 --lop $cond_flavour.dist_flavour.lop
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
rnateam
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47 --lep $cond_flavour.dist_flavour.lep
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
rnateam
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48 --lexp $cond_flavour.dist_flavour.lexp
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
rnateam
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49 #elif $cond_flavour.dist_flavour.distance_method == '--genafpair'
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
rnateam
parents: 5
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50 --weighti $cond_flavour.dist_flavour.weighti
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
rnateam
parents: 5
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51 --lop $cond_flavour.dist_flavour.lop
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
rnateam
parents: 5
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52 --lep $cond_flavour.dist_flavour.lep
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
rnateam
parents: 5
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53 --lexp $cond_flavour.dist_flavour.lexp
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
rnateam
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54 --LOP $cond_flavour.dist_flavour.skipLOP
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
rnateam
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55 --EXP $cond_flavour.dist_flavour.skipEXP 1
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
rnateam
parents: 5
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56 #elif $cond_flavour.dist_flavour.distance_method == '--fastapair'
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
rnateam
parents: 5
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57 --weighti $cond_flavour.dist_flavour.weighti
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
rnateam
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58 #end if
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
rnateam
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59 --maxiterate $cond_flavour.iterations
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
rnateam
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60 $cond_flavour.fft
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
rnateam
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61 $cond_flavour.score
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
rnateam
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62 #end if
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
rnateam
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63
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
rnateam
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64 ## specify threads to use
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
rnateam
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65 --thread \${GALAXY_SLOTS:-1}
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
rnateam
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66 $datatype
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
rnateam
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67 --ep $ep
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
rnateam
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68 --op $op
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
rnateam
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69
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
rnateam
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70 #if $matrix_condition.matrix == "BLOSUM"
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
rnateam
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71 --bl $matrix_condition.BLOSUM
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
rnateam
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72 #elif $matrix_condition.matrix == "PAM"
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
rnateam
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73 --jtt $matrix_condition.PAM
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
rnateam
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74 --tm $matrix_condition.tm
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
rnateam
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75 #elif $matrix_condition.matrix == "custom"
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
rnateam
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76 --aamatrix '$matrix_condition.matrixfile'
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
rnateam
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77 --fmodel $matrix_condition.fmodel
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
rnateam
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78 #end if
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
rnateam
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79
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
rnateam
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80 $reorder
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
rnateam
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81 $getTree
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
rnateam
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82 $outputFormat
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
rnateam
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83 '$inputSequences' > '$outputAlignment';
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
rnateam
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84
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
rnateam
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85 #if $getTree == "--treeout"
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
rnateam
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86 mv '${inputSequences}.tree' '$outputTree';
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87 #end if
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88 ]]>
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89 </command>
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90 <inputs>
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91 <param name="inputSequences" type="data" format="fasta" label="Sequences to align" help="Amino acid or nucleotide sequences in FASTA format."/>
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92 <param name="datatype" type="select" label="Data type">
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93 <option value="">Auto detection</option>
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94 <option value="--nuc">Nucleic acids</option>
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95 <option value="--amino">Amino acids</option>
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96 </param>
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97 <conditional name="cond_flavour">
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98 <param name="flavourType" type="select" label="MAFFT flavour" help="Run mafft with pre-defined input parameters. Specification of these parameters can be found in the help section.">
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99 <option value="mafft --auto">auto</option>
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100 <option value="mafft-fftns" selected="true">fftns</option>
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101 <option value="mafft-fftnsi">fftnsi</option>
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102 <option value="mafft-nwns">nwns</option>
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103 <option value="mafft-nwnsi">nwnsi</option>
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104 <option value="mafft-einsi">einsi</option>
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105 <option value="mafft-ginsi">ginsi</option>
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106 <option value="mafft-linsi">linsi</option>
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107 <option value="mafft-qinsi">qinsi</option>
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108 <option value="mafft-xinsi">xinsi</option>
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109 <option value="custom">Custom Parameters</option>
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110 </param>
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111 <when value="mafft-fftns"/>
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112 <when value="mafft --auto"/>
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113 <when value="mafft-fftnsi"/>
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114 <when value="mafft-nwns"/>
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115 <when value="mafft-nwnsi"/>
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116 <when value="mafft-einsi"/>
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117 <when value="mafft-ginsi"/>
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118 <when value="mafft-linsi"/>
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119 <when value="mafft-qinsi"/>
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120 <when value="mafft-xinsi"/>
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
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121 <when value="custom">
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122 <conditional name="dist_flavour">
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123 <param name="distance_method" type="select" display="radio" label="Distance method" help="Distance method must be chosen regarding your data">
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
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124 <option value="--6merpair" selected="true">Shared 6mers distance (fastest)</option>
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
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125 <option value="--globalpair">Global alignment (Needleman-Wunsch)</option>
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126 <option value="--localpair">Local alignment (Smith-Waterman)</option>
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127 <option value="--genafpair">Local, affine gap cost</option>
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128 <option value="--fastapair">All pairwise alignments are computed with FASTA</option>
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129 </param>
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130 <when value="--6merpair">
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131 <param name="retree" type="integer" value="2" min="1" max="100" label="Guide tree is built this number of times in the progressive stage." help="Valid with 6mer distance" />
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
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132 <conditional name="usetree">
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133 <param name="parttree" type="select" label="Use a fast tree-building method?" help="Recommended for a large number (> ~10,000) of sequences are input" >
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
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134 <option value="--parttree" selected="true">Yes</option>
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
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135 <option value="">No</option>
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136 </param>
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137 <when value="--parttree">
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138 <param name="treedistance" type="select" display="radio" label="Distance method" help="Distance method must be chosen regarding your data">
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
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139 <option value="--fastaparttree" selected="true">Distances based on FASTA</option>
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140 <option value="--dpparttree">Distances based on DP. (Needleman-Wunsch)</option>
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
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141 </param>
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142 <param name="partsize" type="integer" value="50" min="0" max="1000" label="Number of partitions in the PartTree algorithm" />
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
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143 <param name="groupsize" type="integer" value="" min="0" max="1000" label="Do not make alignment larger than ... sequences" />
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144 </when>
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145 <when value=""/>
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146 </conditional>
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147 </when>
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148 <when value="--globalpair">
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149 <param name="weighti" type="float" value="2.7" min="1" max="100" label="Weighting factor for the consistency term calculated from pairwise alignments." help="Valid when either of --globalpair, --localpair, --genafpair, --fastapair or --blastpair is selected." />
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
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150 </when>
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151 <when value="--localpair">
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152 <param name="weighti" type="float" value="2.7" min="1" max="100" label="Weighting factor for the consistency term calculated from pairwise alignments." help="Valid when either of --globalpair, --localpair, --genafpair, --fastapair or --blastpair is selected." />
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
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153 <param name="lop" type="float" value="-2.0" label="Gap opening penalty at local pairwise alignment" help="-2.00 default value" />
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154 <param name="lep" type="float" value="0.1" label="Offset value at local pairwise alignment" help="0.1 default value" />
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155 <param name="lexp" type="float" value="-0.1" label="Gap extension penalty at local pairwise alignment." help="-0.1 default value" />
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156 </when>
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157 <when value="--genafpair">
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158 <param name="weighti" type="float" value="2.7" min="1" max="100" label="Weighting factor for the consistency term calculated from pairwise alignments." help="Valid when either of --globalpair, --localpair, --genafpair, --fastapair or --blastpair is selected." />
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
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159 <param name="lop" type="float" value="-2.0" label="Gap opening penalty at local pairwise alignment" help="-2.00 default value" />
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160 <param name="lep" type="float" value="0.1" label="Offset value at local pairwise alignment" help="0.1 default value" />
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
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161 <param name="lexp" type="float" value="-0.1" label="Gap extension penalty at local pairwise alignment." help="-0.1 default value" />
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162 <param name="skipLOP" type="float" value="-6.00" label="Gap opening penalty to skip the alignment" help="-6.00 default value" />
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163 <param name="skipEXP" type="float" value="0.00" label="Gap extension penalty to skip the alignment" help="0 default value" />
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164 </when>
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165 <when value="--fastapair">
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166 <param name="weighti" type="float" value="2.7" min="1" max="100" label="Weighting factor for the consistency term calculated from pairwise alignments." help="Valid when either of --globalpair, --localpair, --genafpair, --fastapair or --blastpair is selected." />
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
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167 </when>
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168 </conditional>
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169 <param name="iterations" type="integer" value="0" min="0" max="1000" label="Maximum number of iterations" help="1000 for maximum quality" />
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
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170 <param name="fft" type="boolean" truevalue="--fft" falsevalue="--nofft" checked="True" label="Use FFT approximation in group-to-group alignment?" />
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171 <param name="score" type="boolean" truevalue="" falsevalue="--noscore" checked="True" label="Check alignment score in the iterative refinement stage?" />
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
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172 </when>
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173 </conditional>
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174 <param name="ep" type="float" value="0.0" label="Gap extend penalty for group-to-group alignment" help="Offset value, which works like gap extension penalty, for group-to-group alignment. For E-INS-i, 0 is recommended to allow large gaps" />
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
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175 <param name="op" type="float" value="1.53" label="Gap opening penalty at group-to-group alignment." help="1.53 default value" />
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
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176 <conditional name="matrix_condition">
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177 <param name="matrix" type="select" label="Matrix selection" display="radio" help="Usefull only for amino acids" >
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178 <option value="">No matrix</option>
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179 <option value="BLOSUM" selected="true">BLOSUM</option>
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180 <option value="PAM">PAM</option>
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181 <option value="custom">Custom</option>
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182 </param>
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183 <when value=""/>
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184 <when value="BLOSUM">
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185 <param name="BLOSUM" type="select" display="radio" label="Coefficient of the BLOSUM matrix">
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
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186 <option value="30">30</option>
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187 <option value="45">45</option>
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188 <option value="62" selected="true">62</option>
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
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189 <option value="80">80</option>
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190 </param>
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191 </when>
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
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192 <when value="PAM">
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193 <param name="PAM" type="integer" value="80" min="1" max="350" label="Coefficient of the JTT PAM matrix" />
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
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194 <param name="tm" type="integer" value="80" min="1" max="350" label="Coefficient of the transmembrane PAM matrix" />
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
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195 </when>
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196 <when value="custom">
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197 <param name="matrixfile" type="data" format="txt" label="User-defined AA scoring matrix" help="The format of matrixfile is the same to that of BLAST. Ignored when nucleotide sequences are input."/>
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
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198 <param name="fmodel" type="boolean" truevalue="--fmodel" falsevalue="" checked="False" label="Incorporate the AA/nuc composition information into the scoring matrix?" />
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
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199 </when>
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200 </conditional>
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201 <param name="reorder" type="boolean" truevalue="--reorder" falsevalue="" checked="False" label="Reorder output?" />
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
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202 <param name="getTree" type="boolean" truevalue="--treeout" falsevalue="" checked="False" label="Display alignment tree ?" />
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
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203 <param name="outputFormat" type="select" label="Output format" help="Either FASTA or ClustalW">
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
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204 <option value="" selected="true">FASTA</option>
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205 <option value="--clustalout">ClustalW</option>
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
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206 <option value="--phylipout">Phylip</option>
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
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207 </param>
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208 </inputs>
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209 <outputs>
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210 <data format="fasta" name="outputAlignment" label="${tool.name} on ${on_string}">
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
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211 <change_format>
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212 <when input="outputFormat" value="--clustalout" format="clustal"/>
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
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213 <when input="outputFormat" value="--phylipout" format="phylip"/>
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
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214 </change_format>
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215 </data>
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
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216 <data name="outputTree" format="txt" label="${tool.name} Guide Tree">
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
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217 <filter>getTree == True</filter>
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218 </data>
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219 </outputs>
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220 <tests>
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221 <test expect_num_outputs="1" >
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222 <param name="inputSequences" value="sample.fa"/>
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223 <param name="flavourType" value="mafft-fftns"/>
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
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224 <param name="outputFormat" value=""/>
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
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225 <output name="outputAlignment" ftype="fasta" file="mafft_fftns_result.aln"/>
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
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226 </test>
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227 <test expect_num_outputs="1" >
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
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228 <param name="inputSequences" value="sample.fa"/>
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229 <param name="flavourType" value="mafft-nwns"/>
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230 <param name="outputFormat" value="--clustalout"/>
8
4de39704d423 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit 7f48fa9f0c2ef08ffe621a8215ea307ab780b9b5"
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231 <output name="outputAlignment" ftype="clustal" file="mafft_nwns_result.aln" lines_diff="2" />
7
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
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232 </test>
14
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233 <!-- WARNING: the results of the following test depends on #threads.
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234 The result seems deterministic for single threaded execution, i.e. GALAXY_SLOTS=1 planemo test
6f28e90db932 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit 1570f3a28232b4b88385cdfbb68f79d80ff1dabb
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235 However, GH CI/CD uses 2 threads and results vary -->
7
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236 <test expect_num_outputs="1" >
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
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237 <param name="inputSequences" value="sample.fa"/>
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238 <param name="flavourType" value="custom"/>
14
6f28e90db932 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit 1570f3a28232b4b88385cdfbb68f79d80ff1dabb
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239 <conditional name="matrix_condition">
6f28e90db932 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit 1570f3a28232b4b88385cdfbb68f79d80ff1dabb
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240 <param name="matrix" value="BLOSUM"/>
6f28e90db932 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit 1570f3a28232b4b88385cdfbb68f79d80ff1dabb
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241 </conditional>
7
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
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242 <param name="BLOSUM" value="62"/>
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
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243 <param name="distance_method" value="--fastapair"/>
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
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244 <param name="weighti" value="2.7"/>
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245 <param name="iterations" value="1000"/>
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
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246 <param name="outputFormat" value="--clustalout"/>
14
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247 <output name="outputAlignment" ftype="clustal" file="mafft_custom_result.aln" compare="sim_size">
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248 <assert_contents>
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249 <has_n_lines n="458" delta="0"/>
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250 <has_text text="CLUSTAL format alignment by MAFFT F-INS-i"/>
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251 <has_text text="NPIVYGISHPKY"/>
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252 <has_text text="1=="/>
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253 <has_text text="36=="/>
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254 <has_line line="8=opsin, ------------------------------------------------------------"/>
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255 </assert_contents>
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256 </output>
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257 </test>
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258 </tests>
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259 <help> <![CDATA[
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260 **What it does**
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261
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262 MAFFT is a multiple sequence alignment program for unix-like operating systems.
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263 It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of <∼200 sequences),
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264 FFT-NS-2 (fast; for alignment of <∼30,000 sequences), etc.
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265 From the MAFFT man page, an overview of the different predefined flavours of the tool is as follows:
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266
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267 **Accuracy-oriented methods:**
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268
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269 - L-INS-i (probably most accurate; recommended for <200 sequences; iterative refinement method incorporating local pairwise alignment information):
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270 - mafft --localpair --maxiterate 1000 input [> output]
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271 - G-INS-i (suitable for sequences of similar lengths; recommended for <200 sequences; iterative refinement method incorporating global pairwise alignment information):
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272 - mafft --globalpair --maxiterate 1000 input [> output]
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273 - E-INS-i (suitable for sequences containing large unalignable regions; recommended for <200 sequences):
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274 - mafft --ep 0 --genafpair --maxiterate 1000 input [> output]. For E-INS-i, the --ep 0 option is recommended to allow large gaps.
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275
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276 **Speed-oriented methods:**
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277
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278 - FFT-NS-i (iterative refinement method; two cycles only):
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279 - mafft --retree 2 --maxiterate 2 input [> output]
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280 - FFT-NS-i (iterative refinement method; max. 1000 iterations):
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281 - mafft --retree 2 --maxiterate 1000 input [> output]
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282 - FFT-NS-2 (fast; progressive method):
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283 - mafft --retree 2 --maxiterate 0 input [> output]
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284 - FFT-NS-1 (very fast; recommended for >2000 sequences; progressive method with a rough guide tree):
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285 - mafft --retree 1 --maxiterate 0 input [> output]
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286 - NW-NS-i (iterative refinement method without FFT approximation; two cycles only):
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287 - mafft --retree 2 --maxiterate 2 --nofft input [> output]
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288 - NW-NS-2 (fast; progressive method without the FFT approximation):
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289 - mafft --retree 2 --maxiterate 0 --nofft input [> output]
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290 - NW-NS-PartTree-1 (recommended for ~10,000 to ~50,000 sequences; progressive method with the PartTree algorithm):
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291 - mafft --retree 1 --maxiterate 0 --nofft --parttree input [> output]
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292
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293 **Options:**
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294
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295 - --auto Automatically selects an appropriate strategy from L-INS-i, FFT-NS-i and FFT-NS-2, according to data size. Default: off (always FFT-NS-2)
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296 - --adjustdirection Generate reverse complement sequences, as necessary, and align them together with the remaining sequences. In the case of protein alignment, these options are just ignored.
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297 - --op Gap opening penalty, default: 1.53
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298 - --ep Offset (works like gap extension penalty), default: 0.0
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299 - --maxiterate Maximum number of iterative refinement, default: 0
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300 - --clustalout Output: clustal format, default: fasta
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301 - --retree number Guide tree is built number times in the progressive stage. Valid with 6mer distance. Default: 2
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302 ]]>
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303 </help>
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304 <expand macro="citations" />
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305 </tool>