Mercurial > repos > petr-novak > various_galaxy_tools

annotate extract_GFF_Features.xml @ 1:639c0edb7e64 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 12:59:20 +0000
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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 <command>
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4 python '$__tool_directory__'/extract_GFF_Features.py $input1 $out_file1 ${column_choice.col} ${column_choice.feature}</command>
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5 <inputs>
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6 <param format="gff" name="input1" type="data" label="Select GFF data"/>
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7 <conditional name="column_choice">
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8 <param name="col" type="select" label="From">
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9 <option value="0" selected="true">Column 1 / Sequence name</option>
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10 <option value="1">Column 2 / Source</option>
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11 <option value="2">Column 3 / Feature</option>
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12 <option value="6">Column 7 / Strand</option>
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13 <option value="7">Column 8 / Frame</option>
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14 </param>
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15 <when value="0">
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16 <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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17 <options from_dataset="input1">
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18 <column name="name" index="0"/>
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19 <column name="value" index="0"/>
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20 <filter type="unique_value" name="unique" column="0"/>
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21 </options>
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22 </param>
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23 </when>
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24 <when value="1">
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25 <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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26 <options from_dataset="input1">
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27 <column name="name" index="1"/>
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28 <column name="value" index="1"/>
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29 <filter type="unique_value" name="unique" column="1"/>
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30 </options>
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31 </param>
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32 </when>
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33 <when value="2">
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34 <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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35 <options from_dataset="input1">
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36 <column name="name" index="2"/>
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37 <column name="value" index="2"/>
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38 <filter type="unique_value" name="unique" column="2"/>
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39 </options>
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40 </param>
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41 </when>
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42 <when value="6">
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43 <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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44 <options from_dataset="input1">
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45 <column name="name" index="6"/>
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46 <column name="value" index="6"/>
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47 <filter type="unique_value" name="unique" column="6"/>
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48 </options>
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49 </param>
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50 </when>
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51 <when value="7">
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52 <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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53 <options from_dataset="input1">
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54 <column name="name" index="7"/>
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55 <column name="value" index="7"/>
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56 <filter type="unique_value" name="unique" column="7"/>
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57 </options>
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58 </param>
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59 </when>
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60 </conditional>
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61 </inputs>
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62 <outputs>
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63 <data format="input" name="out_file1" metadata_source="input1"/>
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64 </outputs>
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65 <tests>
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66 <test>
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67 <param name="input1" value="5.gff"/>
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68 <param name="col" value="0" />
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69 <param name="feature" value="chr5,chr6,chr7,chr8" />
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70 <output name="out_file1" file="Extract_features1_out.gff"/>
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71 </test>
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72 </tests>
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73 <help>
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74
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75 **What it does**
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76
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77 This tool extracts selected features from GFF data.
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78
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79 -----
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80
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81 **Example**
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82
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83 Selecting **promoter** from the following GFF data::
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84
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85 chr22 GeneA enhancer 10000000 10001000 500 + . TGA
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86 chr22 GeneA promoter 10010000 10010100 900 + . TGA
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87 chr22 GeneB promoter 10020000 10025000 400 - . TGB
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88 chr22 GeneB CCDS2220 10030000 10065000 800 - . TGB
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89
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90 will produce the following output::
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91
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92 chr22 GeneA promoter 10010000 10010100 900 + . TGA
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93 chr22 GeneB promoter 10020000 10025000 400 - . TGB
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94
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95 ----
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96
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97 .. class:: infomark
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98
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99 **About formats**
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100
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101 **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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102
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103 1. seqname - Must be a chromosome or scaffold.
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104 2. source - The program that generated this feature.
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105 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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106 4. start - The starting position of the feature in the sequence. The first base is numbered 1.
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107 5. end - The ending position of the feature (inclusive).
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108 6. score - A score between 0 and 1000. If there is no score value, enter ".".
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109 7. strand - Valid entries include '+', '-', or '.' (for don't know/care).
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110 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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111 9. group - All lines with the same group are linked together into a single item.
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112
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113
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114 </help>
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115 </tool>