Mercurial > repos > iuc > qiime_pick_rep_set

annotate pick_rep_set.xml @ 5:8218f848c2b9 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
author iuc
date Sat, 05 Aug 2017 07:27:17 -0400
parents 6ebade612aa0
children 7cba5f38ec6e
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1 <tool id="qiime_pick_rep_set" name="Pick representative set of sequences" version="@WRAPPER_VERSION@.0">
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2 <description> (pick_rep_set)</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_rep_set.py --version</version_command>
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8 <command detect_errors="aggressive"><![CDATA[
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9 pick_rep_set.py
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10 --input_file '$input_file'
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11 #if $picking.type == "de_novo"
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12 --fasta_file '$picking.fasta_file'
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13 #else if $picking.type == "preferred"
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14 --reference_seqs_fp '$picking.reference_seqs_fp'
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15 #if $picking.fasta_file
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16 --fasta_file '$picking.fasta_file'
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17 #end if
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18 #end if
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19 --rep_set_picking_method '$rep_set_picking_method'
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20 --sort_by '$sort_by'
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21 --result_fp '$result_fp'
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22 --log_fp '$log_fp'
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23 ]]></command>
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24 <inputs>
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25 <param argument="--input_file" type="data" format="txt" label="Input OTU mapping file"/>
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26 <conditional name="picking">
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27 <param name="type" type="select" label="Type of OTU picking">
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28 <option value="de_novo">Picking a representative set for de novo-picked OTUs</option>
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29 <option value="preferred">Picking OTUs with "preferred representative" sequence</option>
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30 </param>
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31 <when value="de_novo">
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32 <param argument="--fasta_file" type="data" format="fasta" label="Input fasta file with all of the sequences whose identifiers are listed in the OTU map"/>
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33 </when>
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34 <when value="preferred">
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35 <param argument="--reference_seqs_fp" type="data" format="fasta" label="Collection of preferred representative sequences "/>
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36 <param argument="--fasta_file" type="data" format="fasta" optional="True" label="Input fasta file with all of the sequences whose identifiers are listed in the OTU map" help="If new clusters were allowed"/>
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37 </when>
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38 </conditional>
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39 <param argument="--rep_set_picking_method" type="select" label="Method for picking representative sets">
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40 <option value="random">random</option>
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41 <option value="longest">longest</option>
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42 <option value="most_abundant">most_abundant</option>
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43 <option value="first" selected="true">first (chooses cluster seed when picking otus with uclust)</option>
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44 </param>
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45 <param argument="--sort_by" type="select" label="Sorting by">
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46 <option value="otu" selected="true">OTU</option>
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47 <option value="seq_id">Sequence id</option>
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48 </param>
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49 </inputs>
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50 <outputs>
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51 <data format="fasta" name="result_fp" label="${tool.name} on ${on_string}: Representative sequences"/>
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52 <data format="txt" name="log_fp" label="${tool.name} on ${on_string}: Log"/>
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53 </outputs>
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54 <tests>
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55 <test>
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56 <param name="input_file" value="pick_rep_set/seqs_otus.txt"/>
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57 <param name="type" value="de_novo"/>
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58 <param name="fasta_file" value="pick_rep_set/seqs.fna"/>
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59 <param name="rep_set_picking_method" value="first"/>
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60 <param name="sort_by" value="otu"/>
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61 <output name="result_fp" file="pick_rep_set/first_otu_fasta.fasta"/>
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62 <output name="log_fp">
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63 <assert_contents>
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64 <has_text text="GenericRepSetPicker"/>
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65 <has_text text="Algorithm:first"/>
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66 </assert_contents>
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67 </output>
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68 </test>
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69 <test>
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70 <param name="input_file" value="pick_rep_set/seqs_otus.txt"/>
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71 <param name="type" value="preferred"/>
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72 <param name="fasta_file" value="pick_rep_set/seqs.fna"/>
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73 <param name="reference_seqs_fp" value="pick_rep_set/refseqs.fasta"/>
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74 <param name="rep_set_picking_method" value="first"/>
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75 <param name="sort_by" value="otu"/>
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76 <output name="result_fp" file="pick_rep_set/first_otu_fasta_ref.fasta"/>
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77 <output name="log_fp">
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78 <assert_contents>
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79 <has_text text="ReferenceRepSetPicker"/>
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80 <has_text text="Algorithm:first"/>
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81 </assert_contents>
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82 </output>
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83 </test>
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84 <test>
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85 <param name="input_file" value="pick_rep_set/seqs_otus.txt"/>
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86 <param name="type" value="de_novo"/>
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87 <param name="fasta_file" value="pick_rep_set/seqs.fna"/>
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88 <param name="rep_set_picking_method" value="longest"/>
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89 <param name="sort_by" value="otu"/>
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90 <output name="result_fp" file="pick_rep_set/longest_otu_fasta.fasta"/>
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91 <output name="log_fp">
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92 <assert_contents>
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93 <has_text text="GenericRepSetPicker"/>
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94 <has_text text="Algorithm:longest"/>
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95 </assert_contents>
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96 </output>
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97 </test>
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98 <test>
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99 <param name="input_file" value="pick_rep_set/seqs_otus.txt"/>
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100 <param name="type" value="de_novo"/>
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101 <param name="fasta_file" value="pick_rep_set/seqs.fna"/>
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102 <param name="rep_set_picking_method" value="most_abundant"/>
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103 <param name="sort_by" value="otu"/>
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104 <output name="result_fp" file="pick_rep_set/most_abundant_otu_fasta.fasta"/>
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105 <output name="log_fp">
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106 <assert_contents>
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107 <has_text text="GenericRepSetPicker"/>
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108 <has_text text="Algorithm:most_abundant"/>
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109 </assert_contents>
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110 </output>
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111 </test>
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112 <test>
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113 <param name="input_file" value="pick_rep_set/seqs_otus.txt"/>
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114 <param name="type" value="de_novo"/>
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115 <param name="fasta_file" value="pick_rep_set/seqs.fna"/>
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116 <param name="rep_set_picking_method" value="random"/>
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117 <param name="sort_by" value="otu"/>
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118 <output name="result_fp">
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119 <assert_contents>
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120 <has_text text="1 PC.636_263"/>
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121 <has_text text="101 PC.634_99"/>
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122 </assert_contents>
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123 </output>
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124 <output name="log_fp">
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125 <assert_contents>
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126 <has_text text="GenericRepSetPicker"/>
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127 <has_text text="Algorithm:random"/>
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128 </assert_contents>
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129 </output>
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130 </test>
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131 <test>
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132 <param name="input_file" value="pick_rep_set/seqs_otus.txt"/>
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133 <param name="type" value="de_novo"/>
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134 <param name="fasta_file" value="pick_rep_set/seqs.fna"/>
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135 <param name="rep_set_picking_method" value="first"/>
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136 <param name="sort_by" value="seq_id"/>
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137 <output name="result_fp" file="pick_rep_set/first_seq_id_fasta.fasta"/>
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138 <output name="log_fp">
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139 <assert_contents>
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140 <has_text text="GenericRepSetPicker"/>
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141 <has_text text="Algorithm:first"/>
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142 </assert_contents>
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143 </output>
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144 </test>
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145 </tests>
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146 <help><![CDATA[
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147 **What it does**
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148
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149 After picking OTUs, you can then pick a representative set of sequences. For each OTU, you will end up with one sequence that can be used in subsequent analyses.
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150
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151 The output from pick_rep_set.py is a single FASTA file containing one sequence per OTU. The FASTA header lines will be the OTU identifier (from here on used as the unique sequence identifier) followed by a space, followed by the sequence identifier originally associated with the representative sequence. The name of the output FASTA file will be <input_sequences_filepath>_rep_set.fasta by default, or can be specified via the "-o" parameter.
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152 ]]></help>
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153 <citations>
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154 <expand macro="citations"/>
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155 </citations>
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156 </tool>