Mercurial > repos > iuc > mothur_pairwise_seqs

annotate pairwise.seqs.xml @ 3:cc74f42d74a2 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
author iuc
date Wed, 14 Feb 2018 09:29:51 -0500
parents 4f382764768a
children 74461a54c0cf
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4e1ecccf9ab0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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1 <tool profile="16.07" id="mothur_pairwise_seqs" name="Pairwise.seqs" version="@WRAPPER_VERSION@.0">
4e1ecccf9ab0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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2 <description>calculate uncorrected pairwise distances between sequences</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <expand macro="stdio"/>
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8 <expand macro="version_command"/>
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9 <command><![CDATA[
3
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10 @SHELL_OPTIONS@
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11
3
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12 ## create symlinks to input datasets
cc74f42d74a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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13 ln -s '$fasta' fasta.dat &&
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14
3
cc74f42d74a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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15 echo 'pairwise.seqs(
cc74f42d74a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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16 fasta=fasta.dat,
cc74f42d74a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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17 align=$align,
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18 #if $calc:
cc74f42d74a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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19 calc=$calc,
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20 #end if
cc74f42d74a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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21 $countends
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22 #if float($cutoff) > 0.0:
cc74f42d74a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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23 cutoff=$cutoff,
cc74f42d74a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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24 #end if
cc74f42d74a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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25 #if $scoring.setby == "user":
cc74f42d74a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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26 match=$scoring.match,
cc74f42d74a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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27 mismatch=$scoring.mismatch,
cc74f42d74a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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28 gapopen=$scoring.gapopen,
cc74f42d74a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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29 gapextend=$scoring.gapextend,
cc74f42d74a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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30 #end if
cc74f42d74a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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31 #if $output:
cc74f42d74a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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32 output=$output,
cc74f42d74a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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33 #end if
cc74f42d74a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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34 processors='\${GALAXY_SLOTS:-8}'
cc74f42d74a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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35 )'
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36 | sed 's/ //g' ## mothur trips over whitespace
cc74f42d74a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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37 | mothur
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38 | tee mothur.out.log
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39 ]]></command>
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40 <inputs>
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41 <param name="fasta" type="data" format="fasta" label="fasta - Fasta"/>
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42 <param name="align" type="select" label="align - Select a pairwise alignment method" help="">
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43 <option value="needleman" selected="true">needleman (default)</option>
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44 <option value="gotoh">gotoh</option>
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45 <option value="blast">blast</option>
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46 </param>
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47 <param name="calc" type="select" label="calc - Calc Method - Gap Penality" help="">
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48 <option value="" selected="true">use default</option>
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49 <option value="onegap">onegap - counts a string of gaps as a single gap</option>
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50 <option value="nogaps">nogaps - ignores gaps</option>
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51 <option value="eachgap">eachgap - penalize each gap</option>
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52 </param>
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53 <param name="countends" type="boolean" checked="true" truevalue="" falsevalue="countends=false," label="countends - Countends" help="Penalize terminal gaps"/>
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54 <param name="cutoff" type="float" value="0.0" min="0" label="cutoff - Distance Cutoff threshold - ignored if not > 0" help="Do not save any distances larger than this, a common value would be 0.10"/>
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55 <conditional name="scoring">
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56 <param name="setby" type="select" label="Scoring match, mismatch, gapopen, and gapextend" help="">
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57 <option value="default" selected="true">Use default settings</option>
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58 <option value="user">Manually set scoring values</option>
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59 </param>
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60 <when value="default"/>
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61 <when value="user">
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62 <param name="match" type="integer" value="1" label="match - Pairwise alignment reward for a match"/>
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63 <param name="mismatch" type="integer" value="-1" label="mismatch - Pairwise alignment penalty for a mismatch"/>
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64 <param name="gapopen" type="integer" value="-2" label="gapopen - Pairwise alignment penalty for opening a gap"/>
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65 <param name="gapextend" type="integer" value="-1" label="gapextend - Pairwise alignment penalty for extending a gap"/>
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66 </when>
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67 </conditional>
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68 <param name="output" type="select" label="output - Distance Matrix Output Format" help="">
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69 <option value="" selected="true">Column-Formatted Matrix (Default)</option>
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70 <option value="lt">Phylip formatted Lower Triangle Matrix</option>
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71 <option value="square">Phylip formatted Square Matrix</option>
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72 </param>
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73 </inputs>
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74 <outputs>
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75 <expand macro="logfile-output"/>
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76 <data name="out_dist" format="mothur.pair.dist" from_work_dir="fasta*.dist" label="${tool.name} on ${on_string}: dist">
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77 <change_format>
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78 <when input="output" value="lt" format="mothur.lower.dist"/>
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79 <when input="output" value="square" format="mothur.square.dist"/>
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80 </change_format>
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81 </data>
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82 </outputs>
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83 <tests>
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84 <test>
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85 <param name="fasta" value="amazon.unique.fasta"/>
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86 <param name="align" value="needleman"/>
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87 <param name="calc" value=""/>
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88 <param name="countends" value=""/>
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89 <param name="cutoff" value="0.0"/>
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90 <param name="setby" value="default"/>
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91 <param name="output" value=""/>
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92 <expand macro="logfile-test"/>
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93 <output name="out_dist" md5="bb2fefcda217604cd0e985f676168379"/>
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94 </test>
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95 <test>
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96 <param name="fasta" value="amazon.unique.fasta"/>
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97 <param name="align" value="gotoh"/>
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98 <param name="calc" value="onegap"/>
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99 <param name="countends" value="countends=false,"/>
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100 <param name="cutoff" value="0.01"/>
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101 <param name="setby" value="user"/>
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102 <param name="match" value="2"/>
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103 <param name="mismatch" value="-1"/>
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104 <param name="gapopen" value="-2"/>
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105 <param name="gapextend" value="-1"/>
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106 <param name="output" value="lt"/>
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107 <expand macro="logfile-test"/>
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108 <output name="out_dist" md5="945c494bee1700c7f9a4ce5d87355190"/>
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109 </test>
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110 </tests>
3
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111 <help><![CDATA[
0
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112
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113 @MOTHUR_OVERVIEW@
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114
1
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115 .. _Mothur: https://www.mothur.org/wiki/Main_Page
0
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116
1
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117 **Command Documentation**
0
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118
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119 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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120
1
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121 .. _column-formatted_distance_matrix: https://www.mothur.org/wiki/Column-formatted_distance_matrix
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122 .. _phylip-formatted_distance_matrix: https://www.mothur.org/wiki/Phylip-formatted_distance_matrix
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123 .. _pairwise.seqs: https://www.mothur.org/wiki/Pairwise.seqs
0
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124
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125 ]]></help>
0
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126 <expand macro="citations"/>
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127 </tool>