Mercurial > repos > jjohnson > mothur_toolsuite
annotate mothur/tools/mothur/clearcut.xml @ 35:95d75b35e4d2
Updated tools to use Mothur 1.33. Added some misc. fixes and updates (blast repository, tool fixes)
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date | Fri, 31 Oct 2014 15:09:32 -0400 |
parents | 49058b1f8d3f |
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1 <tool id="mothur_clearcut" name="Clearcut" version="1.20.0"> |
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2 <description>Generate a tree using relaxed neighbor joining</description> |
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3 <command interpreter="python"> |
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4 mothur_wrapper.py |
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5 --cmd='clearcut' |
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6 #if $matrixout == True or $matrixout.__str__ == "true": |
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7 --matrixout='matrixout.dist' |
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8 --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.tre$:'$tree,'^matrixout\.dist$:'$matrix |
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9 #else |
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10 --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.tre$:'$tree |
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11 #end if |
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12 --outputdir='$logfile.extra_files_path' |
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13 #if $input.source == 'dna': |
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14 --fasta=$input.fasta |
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15 --DNA=true |
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16 #elif $input.source == 'aa': |
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17 --fasta=$input.fasta |
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18 --protein=true |
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19 #elif $input.source == 'phylip': |
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20 --phylip=$input.dist |
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21 #end if |
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22 #if int($seed.__str__) >= 0: |
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23 --seed=$seed |
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24 #end if |
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25 #if int($ntrees.__str__) > 1: |
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26 --ntrees=$ntrees |
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27 #end if |
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28 $norandom |
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29 $shuffle |
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30 $neighbor |
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31 </command> |
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32 <inputs> |
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33 <!-- get.relabund relabund type should also work --> |
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34 <conditional name="input"> |
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35 <param name="source" type="select" label="Distance Matrix"> |
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36 <option value="dna">DNA Alignment Fasta</option> |
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37 <option value="aa">Protein Alignment Fasta</option> |
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38 <option value="phylip">Phylip Distance Matrix</option> |
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39 </param> |
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40 <when value="dna"> |
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41 <param name="fasta" type="data" format="align" label="fasta - Alignment Fasta"/> |
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42 </when> |
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43 <when value="aa"> |
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44 <param name="fasta" type="data" format="align" label="fasta - Alignment Fasta"/> |
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45 </when> |
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46 <when value="phylip"> |
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47 <param name="dist" type="data" format="lower.dist,square.dist" label="phylip - Distance Matrix"/> |
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48 </when> |
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49 </conditional> |
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50 <param name="seed" type="integer" value="-1" label="seed - Set the PRNG seed to a specific value (ignored if negative)"/> |
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51 <param name="ntrees" type="integer" value="1" label="ntrees - the number of output trees you want clearcut to generate (ignored if < 1)"/> |
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52 <param name="norandom" type="boolean" checked="false" truevalue="--norandom=true" falsevalue="" label="norandom - Attempt joins deterministically"/> |
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53 <param name="shuffle" type="boolean" checked="false" truevalue="--shuffle=true" falsevalue="" label="shuffle - Randomly shuffle the distance matrix"/> |
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54 <param name="neighbor" type="boolean" checked="false" truevalue="--neighbor=true" falsevalue="" label="neighbor - Use traditional Neighbor-Joining algorithm"/> |
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55 <param name="expblen" type="boolean" checked="false" truevalue="--expblen=true" falsevalue="" label="expblen - Use exponential notation for branch lengths"/> |
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56 <param name="expdist" type="boolean" checked="false" truevalue="--expdist=true" falsevalue="" label="expdist - Use exponential notation for distance"/> |
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57 <param name="matrixout" type="boolean" checked="false" truevalue="true" falsevalue="" label="matrixout - Generate a Distance Matrix"/> |
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58 </inputs> |
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59 <outputs> |
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60 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> |
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61 <data format="tre" name="tree" label="${tool.name} on ${on_string}: tree" /> |
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62 <data format="lower.dist" name="matrix" label="${tool.name} on ${on_string}: Phylip Distance Matrix" > |
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63 <filter>matrixout == True</filter> |
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64 </data> |
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65 </outputs> |
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66 <requirements> |
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67 <requirement type="package" version="1.33">mothur</requirement> |
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68 </requirements> |
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69 <tests> |
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70 </tests> |
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71 <help> |
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72 **Mothur Overview** |
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73 |
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74 Mothur_, initiated by Dr. Patrick Schloss and his software development team |
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75 in the Department of Microbiology and Immunology at The University of Michigan, |
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76 provides bioinformatics for the microbial ecology community. |
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77 |
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78 .. _Mothur: http://www.mothur.org/wiki/Main_Page |
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79 |
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80 **Command Documenation** |
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81 |
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82 The clearcut_ command runs clearcut |
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83 |
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84 The clearcut command allows mothur users to run the clearcut_program_ from within mothur. The clearcut program written by Initiative for Bioinformatics and Evolutionary Studies (IBEST) at the University of Idaho. For more information about clearcut please refer to http://bioinformatics.hungry.com/clearcut/ |
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85 |
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86 Clearcut is a stand-alone reference implementation of relaxed neighbor joining (RNJ). |
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87 |
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88 Clearcut is capable of taking either a distance matrix or a multiple sequence alignment (MSA) as input. If necessary, Clearcut will compute corrected distances based on a configurable distance correction model (Jukes-Cantor or Kimura). Clearcut outputs a phylogenetic tree in Newick format and an optional corrected distance matrix. |
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89 |
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90 .. _clearcut_program: http://bioinformatics.hungry.com/clearcut/ |
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91 .. _clearcut: http://www.mothur.org/wiki/Clearcut |
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92 |
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93 v.1.20.0: Trivial upgrade to Mothur 1.33 |
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94 |
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95 </help> |
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96 </tool> |