Mercurial > repos > petr-novak > various_galaxy_tools

annotate extract_GFF_Features.xml @ 2:90c46e40d222 draft

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planemo upload for repository https://github.com/kavonrtep/galaxy_packages commit 248ffeb6792d5807820b664eae3e88306f3f395e-dirty
author petr-novak
date Mon, 26 Feb 2024 13:11:53 +0000
parents 639c0edb7e64
children
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1 <tool id="Extract_features1" name="Extract features" version="1.0.0">
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2 <description>from GFF data</description>
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3 <required_files>
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4 <include type="literal" path="extract_GFF_Features.py"/>
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5 </required_files>
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6 <command>
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7 python '$__tool_directory__'/extract_GFF_Features.py $input1 $out_file1 ${column_choice.col} ${column_choice.feature}</command>
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8 <inputs>
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9 <param format="gff" name="input1" type="data" label="Select GFF data"/>
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10 <conditional name="column_choice">
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11 <param name="col" type="select" label="From">
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12 <option value="0" selected="true">Column 1 / Sequence name</option>
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13 <option value="1">Column 2 / Source</option>
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14 <option value="2">Column 3 / Feature</option>
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15 <option value="6">Column 7 / Strand</option>
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16 <option value="7">Column 8 / Frame</option>
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17 </param>
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18 <when value="0">
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19 <param name="feature" type="select" multiple="true" label="Extract features" help="Multi-select list - hold the appropriate key while clicking to select multiple columns">
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20 <options from_dataset="input1">
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21 <column name="name" index="0"/>
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22 <column name="value" index="0"/>
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23 <filter type="unique_value" name="unique" column="0"/>
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24 </options>
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25 </param>
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26 </when>
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27 <when value="1">
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28 <param name="feature" type="select" multiple="true" label="Extract features" help="Multi-select list - hold the appropriate key while clicking to select multiple columns">
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29 <options from_dataset="input1">
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30 <column name="name" index="1"/>
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31 <column name="value" index="1"/>
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32 <filter type="unique_value" name="unique" column="1"/>
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33 </options>
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34 </param>
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35 </when>
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36 <when value="2">
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37 <param name="feature" type="select" multiple="true" label="Extract features" help="Multi-select list - hold the appropriate key while clicking to select multiple columns">
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38 <options from_dataset="input1">
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39 <column name="name" index="2"/>
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40 <column name="value" index="2"/>
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41 <filter type="unique_value" name="unique" column="2"/>
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42 </options>
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43 </param>
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44 </when>
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45 <when value="6">
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46 <param name="feature" type="select" multiple="true" label="Extract features" help="Multi-select list - hold the appropriate key while clicking to select multiple columns">
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47 <options from_dataset="input1">
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48 <column name="name" index="6"/>
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49 <column name="value" index="6"/>
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50 <filter type="unique_value" name="unique" column="6"/>
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51 </options>
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52 </param>
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53 </when>
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54 <when value="7">
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55 <param name="feature" type="select" multiple="true" label="Extract features" help="Multi-select list - hold the appropriate key while clicking to select multiple columns">
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56 <options from_dataset="input1">
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57 <column name="name" index="7"/>
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58 <column name="value" index="7"/>
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59 <filter type="unique_value" name="unique" column="7"/>
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60 </options>
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61 </param>
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62 </when>
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63 </conditional>
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64 </inputs>
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65 <outputs>
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66 <data format="input" name="out_file1" metadata_source="input1"/>
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67 </outputs>
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68 <tests>
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69 <test>
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70 <param name="input1" value="5.gff"/>
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71 <param name="col" value="0" />
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72 <param name="feature" value="chr5,chr6,chr7,chr8" />
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73 <output name="out_file1" file="Extract_features1_out.gff"/>
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74 </test>
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75 </tests>
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76 <help>
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77
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78 **What it does**
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79
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80 This tool extracts selected features from GFF data.
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81
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82 -----
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83
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84 **Example**
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85
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86 Selecting **promoter** from the following GFF data::
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87
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88 chr22 GeneA enhancer 10000000 10001000 500 + . TGA
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89 chr22 GeneA promoter 10010000 10010100 900 + . TGA
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90 chr22 GeneB promoter 10020000 10025000 400 - . TGB
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91 chr22 GeneB CCDS2220 10030000 10065000 800 - . TGB
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92
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93 will produce the following output::
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94
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95 chr22 GeneA promoter 10010000 10010100 900 + . TGA
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96 chr22 GeneB promoter 10020000 10025000 400 - . TGB
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97
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98 ----
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99
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100 .. class:: infomark
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101
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102 **About formats**
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103
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104 **GFF format** General Feature Format is a format for describing genes and other features associated with DNA, RNA and Protein sequences. GFF lines have nine tab-separated fields::
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105
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106 1. seqname - Must be a chromosome or scaffold.
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107 2. source - The program that generated this feature.
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108 3. feature - The name of this type of feature. Some examples of standard feature types are "CDS", "start_codon", "stop_codon", and "exon".
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109 4. start - The starting position of the feature in the sequence. The first base is numbered 1.
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110 5. end - The ending position of the feature (inclusive).
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111 6. score - A score between 0 and 1000. If there is no score value, enter ".".
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112 7. strand - Valid entries include '+', '-', or '.' (for don't know/care).
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113 8. frame - If the feature is a coding exon, frame should be a number between 0-2 that represents the reading frame of the first base. If the feature is not a coding exon, the value should be '.'.
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114 9. group - All lines with the same group are linked together into a single item.
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115
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116
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117 </help>
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118 </tool>