Mercurial > repos > peterjc > seq_filter_by_id
annotate tools/seq_filter_by_id/seq_filter_by_id.xml @ 10:4a7d8ad2a983 draft
Bump Biopython dependency
author | peterjc |
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date | Thu, 30 Nov 2023 09:50:34 +0000 |
parents | 141612f8c3e3 |
children | 85ef5f5a0562 |
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10 | 1 <tool id="seq_filter_by_id" name="Filter sequences by ID" version="0.2.8"> |
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2 <description>from a tabular file</description> |
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3 <requirements> |
10 | 4 <requirement type="package" version="1.81">biopython</requirement> |
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5 </requirements> |
9 | 6 <version_command> |
7 python $__tool_directory__/seq_filter_by_id.py --version | |
8 </version_command> | |
9 <command detect_errors="aggressive"> | |
10 python $__tool_directory__/seq_filter_by_id.py -i '$input_file' -f '$input_file.ext' | |
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11 #if str($output_choice_cond.output_choice)=="both" |
9 | 12 -p '$output_pos' -n '$output_neg' |
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13 #elif str($output_choice_cond.output_choice)=="pos" |
9 | 14 -p '$output_pos' |
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15 #elif str($output_choice_cond.output_choice)=="neg" |
9 | 16 -n '$output_neg' |
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17 #end if |
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18 #if str($adv_opts.adv_opts_selector)=="advanced" and $adv_opts.strip_suffix |
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19 -s |
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20 #end if |
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21 #if str($id_opts.id_opts_selector)=="tabular": |
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22 ## TODO - Decide on best way to expose multiple ID files via the XML wrapper. |
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23 ## Single tabular file, can call the Python script with either UNION or INTERSECTION |
9 | 24 -l UNION '$id_opts.input_tabular' '$id_opts.columns' |
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25 #else |
9 | 26 -t '$id_opts.id_list' |
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27 #end if |
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28 </command> |
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29 <inputs> |
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30 <param name="input_file" type="data" format="fasta,fastq,sff" label="Sequence file to be filtered" help="FASTA, FASTQ, or SFF format." /> |
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31 <conditional name="id_opts"> |
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32 <param name="id_opts_selector" type="select" label="Filter using the ID list from"> |
10 | 33 <option value="tabular" selected="true">tabular file</option> |
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34 <option value="list">provided list</option> |
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35 <!-- add UNION or INTERSECTION of multiple tabular files here? --> |
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36 </param> |
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37 <when value="tabular"> |
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38 <param name="input_tabular" type="data" format="tabular" label="Tabular file containing sequence identifiers"/> |
10 | 39 <param name="columns" type="data_column" data_ref="input_tabular" multiple="true" numerical="false" |
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40 label="Column(s) containing sequence identifiers" |
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41 help="Multi-select list - hold the appropriate key while clicking to select multiple columns"> |
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42 <validator type="no_options" message="Pick at least one column"/> |
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43 </param> |
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44 </when> |
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45 <when value="list"> |
10 | 46 <param name="id_list" type="text" size="20x80" area="true" format="tabular" |
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47 label="List of sequence identifiers (white space separated)" |
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48 help="You can use both spaces and new lines to separate your identifiers."> |
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49 <sanitizer> |
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50 <valid> |
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51 <!-- default includes underscore, hyphen, etc --> |
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52 <add value="%"/> |
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53 <add value="|"/> |
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54 </valid> |
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55 </sanitizer> |
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56 </param> |
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57 </when> |
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58 </conditional> |
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59 <conditional name="output_choice_cond"> |
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60 <param name="output_choice" type="select" label="Output positive matches, negative matches, or both?"> |
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61 <option value="both">Both positive matches (ID on list) and negative matches (ID not on list), as two files</option> |
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62 <option value="pos">Just positive matches (ID on list), as a single file</option> |
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63 <option value="neg">Just negative matches (ID not on list), as a single file</option> |
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64 </param> |
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65 <!-- Seems need these dummy entries here, compare this to indels/indel_sam2interval.xml --> |
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66 <when value="both" /> |
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67 <when value="pos" /> |
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68 <when value="neg" /> |
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69 </conditional> |
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70 <conditional name="adv_opts"> |
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71 <param name="adv_opts_selector" type="select" label="Advanced Options"> |
10 | 72 <option value="basic" selected="true">Hide Advanced Options</option> |
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73 <option value="advanced">Show Advanced Options</option> |
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74 </param> |
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75 <when value="basic" /> |
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76 <when value="advanced"> |
10 | 77 <param name="strip_suffix" type="boolean" value="false" label="Remove typical pair read name suffixes when matching identifiers?" help="Will remove suffixes including Illumina /1 and /2, Roche 454 .f and .r, and assorted Sanger names like .p* and .q*" /> |
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78 </when> |
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79 </conditional> |
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80 </inputs> |
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81 <outputs> |
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82 <data name="output_pos" format_source="input_file" metadata_source="input_file" label="$input_file.name with matched ID"> |
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83 <filter>output_choice_cond["output_choice"] != "neg"</filter> |
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84 </data> |
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85 <data name="output_neg" format_source="input_file" metadata_source="input_file" label="$input_file.name without matched ID"> |
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86 <filter>output_choice_cond["output_choice"] != "pos"</filter> |
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87 </data> |
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88 </outputs> |
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89 <tests> |
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90 <test> |
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91 <param name="input_file" value="k12_ten_proteins.fasta" ftype="fasta" /> |
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92 <param name="input_tabular" value="k12_hypothetical.tabular" ftype="tabular" /> |
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93 <param name="columns" value="1" /> |
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94 <param name="output_choice" value="pos" /> |
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95 <output name="output_pos" file="k12_hypothetical.fasta" ftype="fasta" /> |
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96 </test> |
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97 <test> |
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98 <param name="input_file" value="k12_ten_proteins.fasta" ftype="fasta" /> |
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99 <param name="input_tabular" value="k12_hypothetical_alt.tabular" ftype="tabular" /> |
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100 <param name="columns" value="1" /> |
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101 <param name="output_choice" value="pos" /> |
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102 <param name="adv_opts_selector" value="advanced" /> |
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103 <param name="strip_suffix" value="true" /> |
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104 <output name="output_pos" file="k12_hypothetical.fasta" ftype="fasta" /> |
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105 </test> |
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106 <test> |
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107 <param name="input_file" value="k12_ten_proteins.fasta" ftype="fasta" /> |
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108 <param name="id_opts_selector" value="list" /> |
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109 <param name="id_list" value="gi|16127999|ref|NP_414546.1|" /> |
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110 <param name="output_choice" value="pos" /> |
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111 <output name="output_pos" file="k12_hypothetical.fasta" ftype="fasta" /> |
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112 </test> |
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113 <test> |
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114 <param name="input_file" value="sanger-pairs-mixed.fastq" ftype="fastq" /> |
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115 <param name="id_opts_selector" value="list" /> |
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116 <param name="id_list" value="WTSI_1055_1a05 WTSI_1055_1g02" /> |
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117 <param name="output_choice" value="pos" /> |
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118 <param name="adv_opts_selector" value="advanced" /> |
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119 <param name="strip_suffix" value="true" /> |
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120 <output name="output_pos" file="sanger-sample.fastq" ftype="fastq" /> |
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121 </test> |
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122 <test> |
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123 <param name="input_file" value="sanger-pairs-mixed.fastq" ftype="fastq" /> |
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124 <param name="id_opts_selector" value="tabular" /> |
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125 <param name="input_tabular" value="sanger-pairs-names.tabular" ftype="tabular" /> |
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126 <param name="columns" value="1" /> |
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127 <param name="output_choice" value="both" /> |
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128 <param name="adv_opts_selector" value="advanced" /> |
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129 <param name="strip_suffix" value="true" /> |
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130 <output name="output_pos" file="sanger-pairs-mixed.fastq" ftype="fastq" /> |
10 | 131 <output name="output_neg" file="empty_file.dat" ftype="fastq" /> |
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132 </test> |
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133 <test> |
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134 <param name="input_file" value="sanger-pairs-mixed.fastq" ftype="fastq" /> |
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135 <param name="input_tabular" value="sanger-pairs-names.tabular" ftype="tabular" /> |
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136 <param name="columns" value="1" /> |
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137 <param name="output_choice" value="both" /> |
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138 <param name="adv_opts_selector" value="advanced" /> |
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139 <param name="strip_suffix" value="false" /> |
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140 <output name="output_pos" file="empty_file.dat" ftype="fastq" /> |
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141 <output name="output_neg" file="sanger-pairs-mixed.fastq" ftype="fastq" /> |
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142 </test> |
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143 </tests> |
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144 <help> |
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145 **What it does** |
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146 |
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147 By default it divides a FASTA, FASTQ or Standard Flowgram Format (SFF) file in |
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148 two, those sequences with or without an ID present in the tabular file column(s) |
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149 specified. You can opt to have a single output file of just the matching records, |
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150 or just the non-matching ones. |
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151 |
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152 Instead of providing the identifiers in a tabular file, you can alternatively |
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153 provide them as a parameter (type or paste them into the text box). This is a |
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154 useful shortcut for extracting a few sequences of interest without first having |
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155 to prepare a tabular file. |
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156 |
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157 Note that the order of sequences in the original sequence file is preserved, as |
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158 is any Roche XML Manifest in an SFF file. Also, if any sequences share an |
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159 identifier (which would be very unusual in SFF files), duplicates are not removed. |
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160 |
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161 **Example Usage** |
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162 |
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163 You may have performed some kind of contamination search, for example running |
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164 BLASTN against a database of cloning vectors or bacteria, giving you a tabular |
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165 file containing read identifiers. You could use this tool to extract only the |
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166 reads without BLAST matches (i.e. those which do not match your contaminant |
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167 database). |
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168 |
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169 You may have a file of FASTA sequences which has been used with some analysis |
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170 tool giving tabular output, which has then been filtered on some criteria. |
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171 You can then use this tool to divide the original FASTA file into those entries |
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172 matching or not matching your criteria (those with or without their identifier |
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173 in the filtered tabular file). |
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174 |
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175 **References** |
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176 |
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177 If you use this Galaxy tool in work leading to a scientific publication please |
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178 cite the following papers: |
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179 |
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180 Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013). |
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181 Galaxy tools and workflows for sequence analysis with applications |
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182 in molecular plant pathology. PeerJ 1:e167 |
10 | 183 https://doi.org/10.7717/peerj.167 |
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184 |
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185 This tool uses Biopython to read and write SFF files, so you may also wish to |
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186 cite the Biopython application note (and Galaxy too of course): |
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187 |
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188 Cock et al (2009). Biopython: freely available Python tools for computational |
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189 molecular biology and bioinformatics. Bioinformatics 25(11) 1422-3. |
10 | 190 https://doi.org/10.1093/bioinformatics/btp163 pmid:19304878. |
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191 |
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192 This tool is available to install into other Galaxy Instances via the Galaxy |
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193 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/seq_filter_by_id |
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194 </help> |
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195 <citations> |
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196 <citation type="doi">10.7717/peerj.167</citation> |
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197 <citation type="doi">10.1093/bioinformatics/btp163</citation> |
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198 </citations> |
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199 </tool> |