Mercurial > repos > jjohnson > mothur_toolsuite

annotate mothur/tools/mothur/pairwise.seqs.xml @ 4:a9d51d14f9e9 draft

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Add tool_dependencies
author Jim Johnson <jj@umn.edu>
date Wed, 05 Sep 2012 21:28:43 -0500
parents 6b358d0f17b4
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1 <tool id="mothur_pairwise_seqs" name="Pairwise.seqs" version="1.19.0">
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2 <description>calculate uncorrected pairwise distances between sequences</description>
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3 <command interpreter="python">
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4 mothur_wrapper.py
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5 --cmd='pairwise.seqs'
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6 --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.dist$:'$out_dist
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7 --outputdir='$logfile.extra_files_path'
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8 --fasta=$fasta
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9 --align=$align
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10 #if len($calc.__str__) > 0:
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11 --calc=$calc
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12 #end if
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13 $countends
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14 #if float($cutoff.__str__) > 0.0:
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15 --cutoff=$cutoff
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16 #end if
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17 #if $scoring.setby == 'user':
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18 --match=$scoring.match
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19 --mismatch=$scoring.mismatch
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20 --gapopen=$scoring.gapopen
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21 --gapextend=$scoring.gapextend
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22 #end if
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23 #if len($output.__str__) > 0:
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24 --output=$output
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25 #end if
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6b358d0f17b4 Update to Mothur version 1.24
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26 --processors=8
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27 </command>
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28 <inputs>
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29 <param name="fasta" type="data" format="fasta" label="fasta - Fasta"/>
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30 <param name="align" type="select" label="align - Select a pairwise alignment method" help="">
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31 <option value="needleman">needleman (default)</option>
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32 <option value="gotoh">gotoh</option>
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33 <option value="blast">blast</option>
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34 </param>
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35 <param name="calc" type="select" label="calc - Calc Method - Gap Penality" help="">
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36 <option value="">use default</option>
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37 <option value="onegap">onegap - counts a string of gaps as a single gap</option>
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38 <option value="nogaps">nogaps - ignores gaps</option>
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39 <option value="eachgap ">eachgap - penalize each gap</option>
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40 </param>
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41 <param name="countends" type="boolean" checked="true" truevalue="" falsevalue="--countends=false" label="countends - Countends"
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42 help="Penalize terminal gaps"/>
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43 <param name="cutoff" type="float" value="0.0" label="cutoff - Distance Cutoff threshold - ignored if not > 0"
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44 help="Do not save any distances larger than this, a common value would be 0.10"/>
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45
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46 <conditional name="scoring">
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47 <param name="setby" type="select" label="Scoring match, mismatch, gapopen, and gapextend" help="">
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48 <option value="default">Use default settings</option>
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49 <option value="user">Manually set scoring values</option>
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50 </param>
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51 <when value="default"/>
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52 <when value="user">
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53 <param name="match" type="integer" value="1" label="match - Pairwise alignment reward for a match"/>
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54 <param name="mismatch" type="integer" value="-1" label="mismatch - Pairwise alignment penalty for a mismatch"/>
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55 <param name="gapopen" type="integer" value="-2" label="gapopen - Pairwise alignment penalty for opening a gap"/>
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56 <param name="gapextend" type="integer" value="-1" label="gapextend - Pairwise alignment penalty for extending a gap"/>
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57 </when>
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58 </conditional>
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59
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60
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61 <param name="output" type="select" label="output - Distance Matrix Output Format" help="">
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62 <option value="">Default Column-Formatted Matrix</option>
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63 <option value="lt">Phylip formatted Lower Triangle Matrix</option>
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64 <option value="square">Phylip formatted Square Matrix</option>
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65 </param>
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66 </inputs>
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67 <outputs>
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68 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
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69 <data format="pair.dist" name="out_dist" label="${tool.name} on ${on_string}: dist">
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70 <change_format>
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71 <when input="output" value="lt" format="lower.dist" />
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72 <when input="output" value="square" format="square.dist" />
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73 </change_format>
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74 </data>
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75 </outputs>
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76 <requirements>
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a9d51d14f9e9 Add tool_dependencies
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77 <requirement type="package" version="1.24.1">mothur</requirement>
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78 </requirements>
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79 <tests>
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80 </tests>
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81 <help>
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82 **Mothur Overview**
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83
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84 Mothur_, initiated by Dr. Patrick Schloss and his software development team
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85 in the Department of Microbiology and Immunology at The University of Michigan,
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86 provides bioinformatics for the microbial ecology community.
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87
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88 .. _Mothur: http://www.mothur.org/wiki/Main_Page
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89
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90 **Command Documenation**
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91
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92 The pairwise.seqs_ command will calculate uncorrected pairwise distances between sequencesi as a column-formatted_distance_matrix_ or phylip-formatted_distance_matrix_.
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93
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94 .. _column-formatted_distance_matrix: http://www.mothur.org/wiki/Column-formatted_distance_matrix
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95 .. _phylip-formatted_distance_matrix: http://www.mothur.org/wiki/Phylip-formatted_distance_matrix
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96 .. _pairwise.seqs: http://www.mothur.org/wiki/Pairwise.seqs
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97
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98
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99 </help>
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100 </tool>