annotate tools/seq_primer_clip/seq_primer_clip.xml @ 5:530c8d6fedd8 draft

v0.0.15 - internal changes
author peterjc
date Wed, 10 May 2017 13:09:52 -0400
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1 <tool id="seq_primer_clip" name="Primer clip sequences" version="0.0.15">
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2 <description>Trim off 5' or 3' primers</description>
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3 <requirements>
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4 <requirement type="package" version="1.0.1">galaxy_sequence_utils</requirement>
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5 <requirement type="package" version="1.67">biopython</requirement>
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6 </requirements>
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7 <version_command>
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8 python $__tool_directory__/seq_primer_clip.py --version
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9 </version_command>
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10 <command detect_errors="aggressive">
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11 python $__tool_directory__/seq_primer_clip.py $input_file $input_file.ext $primer_fasta $primer_type $mm $min_len $keep_negatives $output_file
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12 </command>
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13 <inputs>
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14 <param name="input_file" type="data" format="fasta,fastq,sff" label="Sequence file to clip" help="FASTA, FASTQ, or SFF format."/>
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15 <param name="primer_fasta" type="data" format="fasta" label="FASTA file containing primer(s)"/>
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16 <param name="primer_type" type="select" label="Type of primers">
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17 <option value="Forward">Forward (5') primers</option>
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18 <option value="Reverse">Reverse (3') primers (given with respect to the forward strand)</option>
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19 <option value="Reverse-complement">Reverse (3') primers (given with respect to the reverse strand)</option>
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20 </param>
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21 <param name="mm" type="integer" value="0" label="How many mismatches to allow? (0, 1 or 2)">
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22 <validator type="in_range" min="0" max="2" />
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23 </param>
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24 <param name="keep_negatives" type="boolean" value="false" label="Keep reads with no matched primer"/>
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25 <param name="min_len" type="integer" label="Minimum length for (clipped) sequences " value="1"/>
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26 </inputs>
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27 <outputs>
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28 <data name="output_file" format_source="input_file" metadata_source="input_file" label="$primer_type primer clipped"/>
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29 </outputs>
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30 <tests>
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31 <test>
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32 <param name="input_file" value="MID4_GLZRM4E04_rnd30.fasta" ftype="fasta" />
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33 <param name="primer_fasta" value="dop_primers.fasta" />
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34 <param name="primer_type" value="Forward" />
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35 <param name="mm" value="2" />
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36 <param name="keep_negatives" value="false" />
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37 <param name="min_len" value="35" />
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38 <output name="output_file" file="MID4_GLZRM4E04_rnd30_fclip.fasta" ftype="fasta" />
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39 </test>
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40 <test>
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41 <param name="input_file" value="MID4_GLZRM4E04_rnd30.fastqsanger" ftype="fastqsanger" />
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42 <param name="primer_fasta" value="dop_primers.fasta" />
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43 <param name="primer_type" value="Forward" />
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44 <param name="mm" value="2" />
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45 <param name="keep_negatives" value="false" />
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46 <param name="min_len" value="35" />
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47 <output name="output_file" file="MID4_GLZRM4E04_rnd30_fclip.fastqsanger" ftype="fastqsanger" />
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48 </test>
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49 <test>
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50 <param name="input_file" value="MID4_GLZRM4E04_rnd30.sff" ftype="sff" />
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51 <param name="primer_fasta" value="dop_primers.fasta" />
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52 <param name="primer_type" value="Forward" />
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53 <param name="mm" value="2" />
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54 <param name="keep_negatives" value="false" />
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55 <param name="min_len" value="35" />
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56 <output name="output_file" file="MID4_GLZRM4E04_rnd30_fclip.sff" ftype="sff" />
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57 </test>
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58 <test>
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59 <param name="input_file" value="MID4_GLZRM4E04_rnd30_fclip.fasta" ftype="fasta" />
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60 <param name="primer_fasta" value="dop_primers.fasta" />
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61 <param name="primer_type" value="Reverse" />
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62 <param name="mm" value="2" />
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63 <param name="keep_negatives" value="true" />
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64 <param name="min_len" value="35" />
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65 <output name="output_file" file="MID4_GLZRM4E04_rnd30_frclip.fasta" ftype="fasta" />
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66 </test>
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67 <test>
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68 <param name="input_file" value="MID4_GLZRM4E04_rnd30_fclip.fastqsanger" ftype="fastqsanger" />
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69 <param name="primer_fasta" value="dop_primers.fasta" />
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70 <param name="primer_type" value="Reverse" />
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71 <param name="mm" value="2" />
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72 <param name="keep_negatives" value="true" />
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73 <param name="min_len" value="35" />
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74 <output name="output_file" file="MID4_GLZRM4E04_rnd30_frclip.fastqsanger" ftype="fastqsanger" />
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75 </test>
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76 <test>
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77 <param name="input_file" value="MID4_GLZRM4E04_rnd30_fclip.sff" ftype="sff" />
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78 <param name="primer_fasta" value="dop_primers.fasta" />
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79 <param name="primer_type" value="Reverse" />
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80 <param name="mm" value="2" />
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81 <param name="keep_negatives" value="true" />
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82 <param name="min_len" value="35" />
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83 <output name="output_file" file="MID4_GLZRM4E04_rnd30_frclip.sff" ftype="sff" />
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84 </test>
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85 </tests>
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86 <help>
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87
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88 **What it does**
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89
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90 Looks for the given primer sequences (within the existing clipped sequence) and
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91 further clips the reads to remove the primers and any preceding/trailing sequence.
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92
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93 Reads containing a forward primer are reduced to just the sequence after (and
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94 excluding) the forward primer.
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95
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96 Reads containing a reverse primer are reduced to just the sequence before (and
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97 excluding) the reverse primer.
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98
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99 Degenerate primers can be specified using the standard IUPAC ambiguity codes,
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100 thus a primer with an N would match A, C, T or G (or any of the IUPAC ambiguity
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101 codes) and so on.
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102
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103 Note that for SFF files only the clip/trim positions are edited - you will still
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104 be able to extract the original full read (with any adapter sequence and poor
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105 quality sequence) if you need to.
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106
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107 .. class:: warningmark
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108
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109 **Note**. This tool was initially written for Roche 454 data, and should also
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110 work fine on Sanger or Ion Torrent as well. However, it is probably too slow
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111 for use on large Illumina datasets.
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112
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113
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114 **Citation**
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115
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116 This tool uses Biopython. If you use this tool in scientific work leading to a
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117 publication, please cite:
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118
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119 Cock et al 2009. Biopython: freely available Python tools for computational
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120 molecular biology and bioinformatics. Bioinformatics 25(11) 1422-3.
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121 http://dx.doi.org/10.1093/bioinformatics/btp163 pmid:19304878.
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122
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123 This tool is available to install into other Galaxy Instances via the Galaxy
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124 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/seq_primer_clip
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125 </help>
4
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126 <citations>
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127 <citation type="doi">10.1093/bioinformatics/btp163</citation>
9b074c1db68e v0.0.14 galaxy_sequence_utils dependency etc
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128 </citations>
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ee5acea162a7 Uploaded v0.0.10, README now using RST, MIT licence, automatic Biopython dependency
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129 </tool>