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1 <tool id="phylo-protpars-id" name="Phylogeny Maximum Parsimony" version="0.1.0">
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2 <description>Gives an option to add a certain informative site (defined by user) for the Maximum Parsimony Tree</description>
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3 <stdio>
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4 <!-- Whatever match this, is not an error -->
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5 <regex match="[Use of uninitialized value*"/>
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6 </stdio>
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7 <command interpreter="perl">
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8 #if $phylogeny.define
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9 phylo-protpars.pl $input $phylogeny.numValues $phylogeny.numRepeats
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10 #else
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11 phylo-protpars.pl $input
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12 #end if
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13 </command>
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14 <inputs>
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15 <param format="fasta" name="input" type="data" label="Source file"/>
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16 <conditional name="phylogeny">
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17 <param name="define" type="boolean" checked="true" label="Define informative site?"/>
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18
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19 <when value="true">
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20 <param name="numValues" type="integer" value="2" min="2" label="Minimum number of different repeated aa. (>1)" />
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21 <param name="numRepeats" type="integer" value="2" min="2" label="Minimum frequency of the aa. (>1)" />
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22 </when>
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23 </conditional>
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24 </inputs>
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25 <outputs>
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26 <data name="output_tree_text" format="txt" label="Tree as text" from_work_dir="treePars.txt"/>
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27 <data name="output_alignment" format="phylip" label="Alignment from ClustalW" from_work_dir="sequences.aln"/>
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28 <data name="output_alignment_phy" format="phylip" label="Alignment processed" from_work_dir="sequences.aln.phy">
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29 <filter>phylogeny['define']</filter>
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30 </data>
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31 </outputs>
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32
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33 <help>
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34 <!-- This tool computes a Maximum Parsimony Tree with specific values given by the user. -->
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35 .. class:: infomark
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36
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37 **Example 1: without informative sites**
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38 source file = 'sequences.fasta'
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39
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40 result::
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41
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42 Tree as text
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43 (2134442,(((1170853,1172622),1169853),1708266));
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44
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45 Alignment from ClustalW
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46 5 376
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47 1708266 ------MTCQ AFASSDNFVP LNSDSSPSLP LIMHHSAAEC LPVSNHATSV
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48 2134442 -----MVPNY STEETVKRIH VDCPVSGRHS YIYIMVPTVY SIIFIIGIFG
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49 1169853 MTLESMMACC LSDEVKESKR INAEIEKQLR RDKRDARREL KLLLLG--TG
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50 1172622 --------MS NTGASLKGLL LAVLLVSNML LTKEGVTSLP ICSSGSVNCQ
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51 1170835 ---------- ---------- ---------- ---------- --------MG
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52
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53 VSTVPSVLSL IQTPKCSHLH FAMMTSGNVS AGLHYSVPSC HYGNQTSTYG
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54 NSLVVIVIYC YMKLKTVASI FLLNLALADL CFLITLPLWA AYTAMEYQWP
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55 ESGKSTFIKQ MRIIHGSGYS EEDKKGFTKL VYQNIFTAMQ SMIRAMETLK
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56 VSLGELFDRA VRLSHYIHFL SSEIFNEFDE RYAQGRGFIT KAVNGCHTSS
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57 GAQVLVLMTL LGTPPVTTGT PPVVVDPSVA VVGPPLGLGG GGRPPCRPIN
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58
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59 **Example 2: with informative sites**
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60 source file = 'sequences.fasta'
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61
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62 Minimum number of different repeated aa. (>1) = 2
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63
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64 Minimum frequency of the aa. (>1) = 2
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65
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66 result::
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67
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68 Tree as text
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69 (2134442,(1172622,(1169853,(1170835,1708266))));
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70
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71 Alignment from ClustalW
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72 5 376
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73 1708266 ------MTCQ AFASSDNFVP LNSDSSPSLP LIMHHSAAEC LPVSNHATSV
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74 2134442 -----MVPNY STEETVKRIH VDCPVSGRHS YIYIMVPTVY SIIFIIGIFG
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75 1169853 MTLESMMACC LSDEVKESKR INAEIEKQLR RDKRDARREL KLLLLG--TG
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76 1172622 --------MS NTGASLKGLL LAVLLVSNML LTKEGVTSLP ICSSGSVNCQ
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77 1170835 ---------- ---------- ---------- ---------- --------MG
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78
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79 VSTVPSVLSL IQTPKCSHLH FAMMTSGNVS AGLHYSVPSC HYGNQTSTYG
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80 NSLVVIVIYC YMKLKTVASI FLLNLALADL CFLITLPLWA AYTAMEYQWP
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81 ESGKSTFIKQ MRIIHGSGYS EEDKKGFTKL VYQNIFTAMQ SMIRAMETLK
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82 VSLGELFDRA VRLSHYIHFL SSEIFNEFDE RYAQGRGFIT KAVNGCHTSS
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83 GAQVLVLMTL LGTPPVTTGT PPVVVDPSVA VVGPPLGLGG GGRPPCRPIN
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84
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85 Alignment processed
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86 5 12
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87 1708266 VKVLQIKRAK QN
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88 2134442 VKDLVVATFK KP
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89 1169853 FHKERIKSFR LS
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90 1172622 FHDEVVASYD KN
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91 1170835 LPV-RRGRAD QP
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92
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93 </help>
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94
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95 </tool>
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