Mercurial > repos > iuc > pick_closed_reference_otus

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
author iuc
date Thu, 18 May 2017 09:37:50 -0400
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768fb40ad1e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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1 <tool id="pick_closed_reference_otus" name="Perform closed-reference OTU picking" version="@WRAPPER_VERSION@.0">
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2 <description></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 <version_command>pick_closed_reference_otus.py --version</version_command>
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8 <command detect_errors="aggressive"><![CDATA[
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9 pick_closed_reference_otus.py
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10 --input_fp '$input_fp'
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11 --output_dir otus
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12 #if str( $ref_seq.selector ) == 'history'
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13 #set $ref = $ref_seq.reference_fp
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14 #else
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15 #set $ref = $ref_seq.reference_fp.fields.path
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16 #end if
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17 --reference_fp '$ref'
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18 #if str( $taxonomy.selector ) == 'taxonomy_map'
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19 #if str( $taxonomy.taxo_map.selector ) == 'history'
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20 #set $taxonomy = $taxonomy.taxo_map.taxonomy_fp
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21 #else
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22 #set $taxonomy = $taxonomy.taxo_map.taxonomy_fp.fields.path
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23 #end if
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24 --taxonomy_fp '$taxonomy'
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25 #else if str( $taxonomy.selector ) == 'assign_taxonomy'
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26 --assign_taxonomy
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27 #else if str( $taxonomy.selector ) == 'suppress_taxonomy_assignment'
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28 --suppress_taxonomy_assignment
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29 #end if
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30 #if $parameter_fp
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31 --parameter_fp '$parameter_fp'
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32 #end if
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33 $parallel
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34 -O "\${GALAXY_SLOTS:-4}"
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35 ]]></command>
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36 <inputs>
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37 <param argument="--input_fp" type="data" format="fasta" label="Input sequence file"/>
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38 <conditional name="ref_seq">
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39 <param name="selector" type="select" label="Reference sequences to query">
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40 <option value="cached" selected="True">Public databases</option>
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41 <option value="history">Databases from your history</option>
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42 </param>
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43 <when value="cached">
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44 <param argument="--reference_fp" label="Reference sequences" type="select">
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45 <options from_data_table="qiime_rep_set"/>
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46 </param>
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47 </when>
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48 <when value="history">
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49 <param argument="--reference_fp" type="data" format="fasta" label="Reference databases"/>
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50 </when>
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51 </conditional>
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52 <conditional name="taxonomy">
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53 <param name="selector" type="select" label="Assign taxonomy?">
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54 <option value="taxonomy_map" selected="True">Assign taxonomy using a taxonomy map</option>
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55 <option value="assign_taxonomy">Assign taxonomy to each sequence using assign_taxonomy.py</option>
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56 <option value="suppress_taxonomy_assignment">Skip the taxonomy assignment step</option>
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57 </param>
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58 <when value="taxonomy_map">
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59 <conditional name="taxo_map">
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60 <param name="selector" type="select" label="Taxonomy map to use">
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61 <option value="cached" selected="True">Public taxonomy map</option>
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62 <option value="history">Taxonomy map from your history</option>
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63 </param>
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64 <when value="cached">
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65 <param argument="--taxonomy_fp" label="Taxonomy map" type="select">
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66 <options from_data_table="qiime_taxonomy"/>
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67 </param>
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68 </when>
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69 <when value="history">
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70 <param argument="--taxonomy_fp" type="data" format="txt" label="Taxonomy map"/>
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71 </when>
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72 </conditional>
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73 </when>
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74 <when value="assign_taxonomy"/>
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75 <when value="suppress_taxonomy_assignment"/>
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76 </conditional>
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77 <param argument="--parameter_fp" type="data" format="txt" optional="true" label="Parameter file" help="It specifies changes to the default behavior"/>
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78 <param argument="--parallel" type="boolean" truevalue="--parallel" falsevalue="" checked="True" label="Run in parallel where available?"/>
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79 </inputs>
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80 <outputs>
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81 <data name="otu_table" format="biom1" from_work_dir="otus/otu_table.biom" label="${tool.name} on ${on_string}: OTU table"/>
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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="input_fps" value="pick_closed_reference_otus/seqs.fna"/>
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86 <conditional name="ref_seq">
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87 <param name="selector" value="history"/>
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88 <param name="reference_fp" value="pick_closed_reference_otus/refseqs.fna"/>
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89 </conditional>
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90 <conditional name="taxonomy">
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91 <param name="selector" value="taxonomy_map"/>
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92 <conditional name="taxo_map">
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93 <param name="selector" value="history"/>
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94 <param name="taxonomy_fp" value="pick_closed_reference_otus/taxa.txt"/>
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95 </conditional>
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96 </conditional>
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97 <param name="parallel" value=""/>
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98 <output name="otu_table" file="pick_closed_reference_otus/basic_otu_table.biom" compare="sim_size" />
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99 </test>
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100 <test>
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101 <param name="input_fps" value="pick_closed_reference_otus/seqs.fna"/>
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102 <conditional name="ref_seq">
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103 <param name="selector" value="history"/>
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104 <param name="reference_fp" value="pick_closed_reference_otus/refseqs.fna"/>
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105 </conditional>
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106 <conditional name="taxonomy">
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107 <param name="selector" value="taxonomy_map"/>
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108 <conditional name="taxo_map">
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109 <param name="selector" value="history"/>
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110 <param name="taxonomy_fp" value="pick_closed_reference_otus/taxa.txt"/>
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111 </conditional>
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112 </conditional>
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113 <param name="parameter_fp" value="pick_closed_reference_otus/sortmerna_params.txt"/>
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114 <param name="parallel" value=""/>
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115 <output name="otu_table" file="pick_closed_reference_otus/sortmerna_otu_table.biom" compare="sim_size" />
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116 </test>
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117 <test>
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118 <param name="input_fps" value="pick_closed_reference_otus/seqs.fna"/>
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119 <conditional name="ref_seq">
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120 <param name="selector" value="history"/>
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121 <param name="reference_fp" value="pick_closed_reference_otus/refseqs.fna"/>
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122 </conditional>
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123 <conditional name="taxonomy">
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124 <param name="selector" value="assign_taxonomy"/>
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125 </conditional>
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126 <param name="parallel" value=""/>
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127 <output name="otu_table" file="pick_closed_reference_otus/assign_taxonomy_otu_table.biom" compare="sim_size" />
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128 </test>
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129 <test>
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130 <param name="input_fps" value="pick_closed_reference_otus/seqs.fna"/>
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131 <conditional name="ref_seq">
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132 <param name="selector" value="history"/>
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133 <param name="reference_fp" value="pick_closed_reference_otus/refseqs.fna"/>
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134 </conditional>
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135 <conditional name="taxonomy">
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136 <param name="selector" value="suppress_taxonomy_assignment"/>
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137 </conditional>
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138 <param name="parallel" value=""/>
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139 <output name="otu_table" file="pick_closed_reference_otus/suppress_taxonomy_assignment_otu_table.biom" compare="sim_size" />
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140 </test>
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141 </tests>
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142 <help><![CDATA[
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143 **What it does**
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144
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145 This script picks OTUs using a closed reference and constructs an OTU table. Taxonomy is assigned using a pre-defined taxonomy map of reference sequence OTU to taxonomy. If full-length genomes are provided as the reference sequences, this script applies the Shotgun UniFrac method.
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146
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147 More information about this tool is available on
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148 `QIIME documentation <http://qiime.org/scripts/pick_closed_reference_otus.html>`_.
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149 ]]></help>
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150 <citations>
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151 <expand macro="citations"/>
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152 </citations>
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153 </tool>