Mercurial > repos > iuc > mothur_classify_seqs

annotate classify.seqs.xml @ 0:0b58880da760 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
author iuc
date Fri, 24 Jun 2016 17:36:48 -0400
parents
children 7c45c65f957b
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0b58880da760 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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1 <tool profile="16.07" id="mothur_classify_seqs" name="Classify.seqs" version="@WRAPPER_VERSION@.0">
0b58880da760 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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2 <description>Assign sequences to taxonomy</description>
0b58880da760 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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3 <macros>
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iuc
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4 <import>macros.xml</import>
0b58880da760 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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5 </macros>
0b58880da760 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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6 <expand macro="requirements"/>
0b58880da760 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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7 <expand macro="version_command"/>
0b58880da760 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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8 <command detect_errors="aggressive"><![CDATA[
0b58880da760 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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9 ## enable mothur to find blast
0b58880da760 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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10 loc=`which mothur` && ln -s "\${loc%/mothur}"/* . &&
0b58880da760 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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11
0b58880da760 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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12 ## create symlinks to input datasets
0b58880da760 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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13 ln -s "$fasta" fasta.dat &&
0b58880da760 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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14 ln -s "$alignment.template" alignment.template.dat &&
0b58880da760 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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15 ln -s "$tax.taxonomy" tax.taxonomy.dat &&
0b58880da760 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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16 ln -s "$count" count.dat &&
0b58880da760 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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17
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18 echo 'classify.seqs(
0b58880da760 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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19 fasta=fasta.dat,
0b58880da760 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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20 reference=alignment.template.dat,
0b58880da760 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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21 taxonomy=tax.taxonomy.dat,
0b58880da760 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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22 method=$classify.method,
0b58880da760 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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23 #if $classify.method == "wang":
0b58880da760 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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24 ksize=$classify.ksize,
0b58880da760 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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25 iters=$classify.iters,
0b58880da760 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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26 cutoff=$classify.cutoff,
0b58880da760 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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27 probs=$classify.probs,
0b58880da760 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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28 #elif $classify.method == "knn":
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29 numwanted=$classify.numwanted,
0b58880da760 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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30 search=$classify.search.algorithm,
0b58880da760 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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31 #if $classify.search.algorithm == "kmer":
0b58880da760 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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32 ksize=$classify.search.ksize,
0b58880da760 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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33 #elif $classify.search.algorithm == "blast":
0b58880da760 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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34 match=$classify.search.match,
0b58880da760 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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35 mismatch=$classify.search.mismatch,
0b58880da760 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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36 gapopen=$classify.search.gapopen,
0b58880da760 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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37 gapextend=$classify.search.gapextend,
0b58880da760 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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38 #end if
0b58880da760 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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39 #end if
0b58880da760 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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40 #if $count:
0b58880da760 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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41 count=count.dat,
0b58880da760 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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42 #end if
0b58880da760 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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43 relabund=$relabund,
0b58880da760 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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44 processors='\${GALAXY_SLOTS:-8}'
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45 )'
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46 | sed 's/ //g' ## mothur trips over whitespace
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47 | ./mothur
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48 ]]></command>
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49 <inputs>
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50 <param name="fasta" type="data" format="fasta" label="fasta - Candiate Sequences"/>
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51 <conditional name="alignment">
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52 <param name="source" type="select" label="Select Reference Template from" help="">
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53 <option value="hist">History</option>
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54 <option value="ref">Cached Reference</option>
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55 </param>
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56 <when value="ref">
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57 <param name="template" type="select" label="reference - Select an alignment database " help="">
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58 <options from_data_table="mothur_aligndb">
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59 </options>
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60 </param>
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61 </when>
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62 <when value="hist">
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63 <param name="template" type="data" format="fasta" label="reference - Reference to align with" help=""/>
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64 </when>
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65 </conditional>
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66 <conditional name="tax">
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67 <param name="source2" type="select" label="Select Taxonomy from" help="">
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68 <option value="ref">Cached Reference</option>
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69 <option value="hist">History</option>
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70 </param>
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71 <when value="ref">
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72 <param name="taxonomy" type="select" format="mothur.seq.taxonomy" label="taxonomy - Taxonomy reference">
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73 <options from_data_table="mothur_taxonomy"/>
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74 </param>
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75 </when>
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76 <when value="hist">
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77 <param name="taxonomy" type="data" format="mothur.seq.taxonomy" label="taxonomy - Taxonomy reference"/>
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78 </when>
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79 </conditional>
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80 <conditional name="classify">
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81 <param name="method" type="select" label="method - Select a classification method" help="">
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82 <option value="wang" selected="true">Bayesian (default)</option>
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83 <option value="knn">K-Nearest Neighbor (knn)</option>
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84 </param>
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85 <when value="wang">
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86 <param name="ksize" type="integer" value="8" min="1" label="ksize - kmer length"/>
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87 <param name="iters" type="integer" value="100" min="1" label="iters - iterations to do when calculating the bootstrap confidence score"/>
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88 <param name="cutoff" type="integer" value="0" min="0" label="cutoff - specify a bootstrap confidence threshold for your taxonomy"/>
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89 <param name="probs" type="boolean" falsevalue="false" truevalue="true" checked="true" label="probs - Show probabilities"/>
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90 </when>
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91 <when value="knn">
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92 <param name="numwanted" type="integer" value="10" label="numwanted - the number of sequence matches you want with the knn method"/>
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93 <conditional name="search">
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94 <param name="algorithm" type="select" label="algorithm - " help="">
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95 <option value="kmer" selected="true">Kmer (default)</option>
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96 <option value="blast">BLAST</option>
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97 <option value="suffix">Suffix Tree</option>
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98 <option value="distance">Distance</option>
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99 </param>
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100 <when value="kmer">
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101 <param name="ksize" type="integer" value="8" min="1" label="ksize - kmer length"/>
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102 </when>
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103 <when value="blast">
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104 <param name="match" type="integer" value="1" label="match - Pairwise alignment reward for a match"/>
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105 <param name="mismatch" type="integer" value="-1" label="mismatch - Pairwise alignment penalty for a mismatch"/>
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106 <param name="gapopen" type="integer" value="-2" label="gapopen - Pairwise alignment penalty for opening a gap"/>
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107 <param name="gapextend" type="integer" value="-1" label="gapextend - Pairwise alignment penalty for extending a gap"/>
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108 </when>
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109 <when value="suffix"/>
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110 <when value="distance"/>
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111 </conditional>
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112 </when>
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113 </conditional>
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114 <param name="count" type="data" format="mothur.count_table" label="count file" optional="true"/>
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115 <param name="relabund" type="boolean" falsevalue="false" truevalue="true" checked="false" label="relabund - allows you to indicate that you want the summary files to be relative abundances rather than raw abundances. default=f"/>
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116 </inputs>
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117 <outputs>
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118 <expand macro="logfile-output"/>
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119 <data name="taxonomy_out" format="mothur.seq.taxonomy" from_work_dir="fasta*.taxonomy" label="${tool.name} on ${on_string}: taxonomy"/>
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120 <data name="tax_summary" format="mothur.tax.summary" from_work_dir="fasta*.tax.summary" label="${tool.name} on ${on_string}: tax.summary"/>
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121 <data name="tree_sum" format="tabular" from_work_dir="tax.taxonomy*.tree.sum" label="${tool.name} on ${on_string}: tree.sum"/>
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122 </outputs>
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123 <tests>
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124 <test><!-- test with wang method -->
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125 <param name="fasta" value="amazon.fasta" ftype="fasta"/>
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126 <param name="source" value="hist"/>
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127 <param name="template" value="abrecovery.fasta" ftype="fasta"/>
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128 <param name="source2" value="hist"/>
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129 <param name="taxonomy" value="abrecovery.pds.wang.taxonomy" ftype="mothur.seq.taxonomy"/>
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130 <output name="tax_summary" md5="d6f02a20cdf415fb84e394d0dab2314f" ftype="mothur.tax.summary"/>
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131 <output name="taxonomy_out" ftype="mothur.seq.taxonomy">
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132 <assert_contents>
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133 <has_text text="Bacteria"/>
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134 <has_text text="U68589"/>
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135 </assert_contents>
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136 </output>
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137 <output name="tree_sum" md5="a6ae5cc82edd181082dd23f348b621d9" ftype="tabular"/>
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138 <expand macro="logfile-test"/>
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139 </test>
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140 <test><!-- test with knn method -->
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141 <param name="fasta" value="amazon.fasta" ftype="fasta"/>
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142 <param name="source" value="hist"/>
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143 <param name="template" value="abrecovery.fasta" ftype="fasta"/>
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144 <param name="source2" value="hist"/>
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145 <param name="taxonomy" value="abrecovery.pds.wang.taxonomy" ftype="mothur.seq.taxonomy"/>
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146 <param name="method" value="knn"/>
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147 <output name="tax_summary" md5="4931072238dcf29344f4a1e3332f3415" ftype="mothur.tax.summary"/>
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148 <output name="taxonomy_out" md5="1080c7676c1a1f4f429c7d8df6a62f47" ftype="mothur.seq.taxonomy"/>
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149 <expand macro="logfile-test"/>
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150 </test>
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151 <test><!-- test with knn method and blast algorithm -->
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152 <param name="fasta" value="abrecovery.fasta" ftype="fasta"/>
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153 <param name="source" value="hist"/>
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154 <param name="template" value="abrecovery.fasta" ftype="fasta"/>
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155 <param name="source2" value="hist"/>
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156 <param name="taxonomy" value="abrecovery.pds.wang.taxonomy" ftype="mothur.seq.taxonomy"/>
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157 <param name="method" value="knn"/>
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158 <param name="algorithm" value="blast"/>
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159 <output name="tax_summary" md5="4d6e1fa3be9abe5f57b0660fe5ae5887" ftype="mothur.tax.summary"/>
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160 <output name="taxonomy_out" md5="1296e2a2c8efd58f9c840760bed55042" ftype="mothur.seq.taxonomy"/>
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161 <expand macro="logfile-test"/>
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162 </test>
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163 </tests>
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164 <help>
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165 <![CDATA[
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166
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167 @MOTHUR_OVERVIEW@
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168
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169 **Command Documenation**
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170
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171 The classify.seqs_ command assigns sequences to chosen taxonomy outline.
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172
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173 .. _classify.seqs: http://www.mothur.org/wiki/Classify.seqs
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174
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175
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176 v1.22.0: Updated for Mothur 1.33. Added count parameter (1.28), added relabund parameter (1.33), bayesian term changed to wang.
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177 ]]>
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178 </help>
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179 <expand macro="citations"/>
0b58880da760 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
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180 </tool>