Mercurial > repos > jjohnson > mothur_toolsuite
annotate mothur/tools/mothur/classify.seqs.xml @ 2:e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
author | jjohnson |
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date | Tue, 07 Jun 2011 17:39:06 -0400 |
parents | fcc0778f6987 |
children | 370b3fc4e7d3 |
rev | line source |
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2
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1 <tool id="mothur_classify_seqs" name="Classify.seqs" version="1.19.0"> |
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2 <description>Assign sequences to taxonomy</description> |
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3 <command interpreter="python"> |
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4 mothur_wrapper.py |
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5 --cmd='classify.seqs' |
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6 --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.taxonomy$:'$taxonomy_out,'^\S+\.tax\.summary$:'$tax_summary |
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7 --outputdir='$logfile.extra_files_path' |
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8 --fasta=$fasta |
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9 --reference=$alignment.template |
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10 --taxonomy=$tax.taxonomy |
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11 #if $classify.method == 'bayesian': |
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12 --method=$classify.method |
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13 #if 15 >= int($classify.ksize.__str__) >= 4: |
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14 --ksize=$classify.ksize |
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15 #end if |
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16 #if int($classify.iters.__str__) > 0: |
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17 --iters=$classify.iters |
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18 #end if |
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19 #if 100 >= int($classify.cutoff.__str__) > 0: |
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20 --cutoff=$classify.cutoff |
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21 #end if |
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22 $classify.probs |
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23 #elif $classify.method == 'knn': |
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24 --method=$classify.method |
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25 --numwanted=$classify.search.numwanted |
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26 #if $classify.search.algorithm == 'kmer': |
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27 --search=$classify.search.algorithm |
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28 --ksize=$classify.search.ksize |
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29 #elif $classify.search.algorithm == 'blast': |
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30 --search=$classify.search.algorithm |
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31 --match=$classify.search.match |
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32 --mismatch=$classify.search.mismatch |
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33 --gapopen=$classify.search.gapopen |
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34 --gapextend=$classify.search.gapextend |
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35 #elif $classify.knn.search == 'suffix': |
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36 --search=$classify.search.algorithm |
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37 #elif $classify.search.algorithm == 'distance': |
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38 --search=$classify.search.algorithm |
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39 #end if |
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40 #end if |
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41 --processors=2 |
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42 </command> |
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43 <inputs> |
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44 <param name="fasta" type="data" format="fasta" label="fasta - Candiate Sequences"/> |
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45 <conditional name="alignment"> |
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46 <param name="source" type="select" label="Select Reference Template from" help=""> |
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47 <option value="hist">History</option> |
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48 <option value="ref">Cached Reference</option> |
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49 </param> |
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50 <when value="ref"> |
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51 <param name="template" type="select" label="reference - Select an alignment database " help=""> |
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52 <options from_file="mothur_aligndb.loc"> |
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53 <column name="name" index="0" /> |
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54 <column name="value" index="1" /> |
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55 </options> |
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56 </param> |
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57 </when> |
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58 <when value="hist"> |
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59 <param name="template" type="data" format="fasta" label="reference - Reference to align with" help=""/> |
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60 </when> |
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61 </conditional> |
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62 <conditional name="tax"> |
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63 <param name="source" type="select" label="Select Taxonomy from" help=""> |
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64 <option value="ref">Cached Reference</option> |
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65 <option value="hist">History</option> |
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66 </param> |
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67 <when value="ref"> |
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68 <param name="taxonomy" type="select" format="seq.taxonomy" label="taxonomy - Taxonomy reference"> |
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69 <options from_file="mothur_taxonomy.loc"> |
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70 <column name="name" index="0" /> |
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71 <column name="value" index="1" /> |
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72 </options> |
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73 </param> |
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74 </when> |
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75 <when value="hist"> |
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76 <param name="taxonomy" type="data" format="seq.taxonomy" label="taxonomy - Taxonomy reference"/> |
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77 </when> |
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78 </conditional> |
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79 <conditional name="classify"> |
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80 <param name="method" type="select" label="method - Select a classification method" help=""> |
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81 <option value="bayesian">Bayesian (default)</option> |
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82 <option value="knn">K-Nearest Neighbor (knn)</option> |
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83 </param> |
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84 <when value="bayesian"> |
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85 <param name="ksize" type="integer" value="8" label="ksize - kmer length between 5 and 12"> |
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86 <validator type="in_range" message="ksize - kmer length between 5 and 12" min="5" max="12"/> |
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87 </param> |
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88 <param name="iters" type="integer" value="100" label="iters - iterations to do when calculating the bootstrap confidence score"/> |
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89 <param name="cutoff" type="integer" value="60" label="cutoff - Confindence percentage cutoff between 1 and 100"> |
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90 <validator type="in_range" message="Confindence percentage cutoff must be between 0 and 100" min="0" max="100"/> |
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91 </param> |
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92 <param name="probs" type="boolean" falsevalue="--probs=false" truevalue="" checked="true" label="probs - Show probabilities"/> |
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93 </when> |
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94 <when value="knn"> |
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95 <param name="numwanted" type="integer" value="10" label="numwanted - "/> |
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96 <conditional name="search"> |
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97 <param name="algorithm" type="select" label="algorithm - " help=""> |
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98 <option value="kmer">Kmer (default)</option> |
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99 <option value="blast">BLAST</option> |
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100 </param> |
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101 <when value="kmer"> |
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102 <param name="ksize" type="integer" value="8" label="ksize - kmer length between 5 and 12"/> |
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103 </when> |
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104 <when value="blast"> |
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105 <param name="match" type="integer" value="1" label="match - Pairwise alignment reward for a match"/> |
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106 <param name="mismatch" type="integer" value="-1" label="mismatch - Pairwise alignment penalty for a mismatch"/> |
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107 <param name="gapopen" type="integer" value="-2" label="gapopen - Pairwise alignment penalty for opening a gap"/> |
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108 <param name="gapextend" type="integer" value="-1" label="gapextend - Pairwise alignment penalty for extending a gap"/> |
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109 </when> |
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110 <when value="suffix"/> |
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111 <when value="distance"/> |
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112 </conditional> |
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113 </when> |
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114 </conditional> |
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115 </inputs> |
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116 <outputs> |
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117 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> |
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118 <data format="seq.taxonomy" name="taxonomy_out" label="${tool.name} on ${on_string}: taxonomy" /> |
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119 <data format="tax.summary" name="tax_summary" label="${tool.name} on ${on_string}: tax.summary" /> |
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120 </outputs> |
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121 <requirements> |
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122 <requirement type="binary">mothur</requirement> |
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123 </requirements> |
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124 <tests> |
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125 </tests> |
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126 <help> |
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127 **Mothur Overview** |
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128 |
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129 Mothur_, initiated by Dr. Patrick Schloss and his software development team |
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130 in the Department of Microbiology and Immunology at The University of Michigan, |
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131 provides bioinformatics for the microbial ecology community. |
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132 |
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133 .. _Mothur: http://www.mothur.org/wiki/Main_Page |
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134 |
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135 **Command Documenation** |
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136 |
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137 The classify.seqs_ command assigns sequences to chosen taxonomy outline. |
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138 |
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139 .. _classify.seqs: http://www.mothur.org/wiki/Classify.seqs |
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140 |
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141 |
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142 </help> |
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143 </tool> |