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comparison extract_GFF_Features.xml @ 0:696e702ebf74 draft

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"planemo upload commit 0f6eca49bafc3c946189d793161a7f81d595e1a1-dirty"
author petr-novak
date Mon, 09 May 2022 08:26:30 +0000
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1 <tool id="Extract_features1" name="Extract features" version="1.0.0">
2 <description>from GFF data</description>
3 <command interpreter="python">extract_GFF_Features.py $input1 $out_file1 ${column_choice.col} ${column_choice.feature}</command>
4 <inputs>
5 <param format="gff" name="input1" type="data" label="Select GFF data"/>
6 <conditional name="column_choice">
7 <param name="col" type="select" label="From">
8 <option value="0" selected="true">Column 1 / Sequence name</option>
9 <option value="1">Column 2 / Source</option>
10 <option value="2">Column 3 / Feature</option>
11 <option value="6">Column 7 / Strand</option>
12 <option value="7">Column 8 / Frame</option>
13 </param>
14 <when value="0">
15 <param name="feature" type="select" multiple="true" label="Extract features" help="Multi-select list - hold the appropriate key while clicking to select multiple columns">
16 <options from_dataset="input1">
17 <column name="name" index="0"/>
18 <column name="value" index="0"/>
19 <filter type="unique_value" name="unique" column="0"/>
20 </options>
21 </param>
22 </when>
23 <when value="1">
24 <param name="feature" type="select" multiple="true" label="Extract features" help="Multi-select list - hold the appropriate key while clicking to select multiple columns">
25 <options from_dataset="input1">
26 <column name="name" index="1"/>
27 <column name="value" index="1"/>
28 <filter type="unique_value" name="unique" column="1"/>
29 </options>
30 </param>
31 </when>
32 <when value="2">
33 <param name="feature" type="select" multiple="true" label="Extract features" help="Multi-select list - hold the appropriate key while clicking to select multiple columns">
34 <options from_dataset="input1">
35 <column name="name" index="2"/>
36 <column name="value" index="2"/>
37 <filter type="unique_value" name="unique" column="2"/>
38 </options>
39 </param>
40 </when>
41 <when value="6">
42 <param name="feature" type="select" multiple="true" label="Extract features" help="Multi-select list - hold the appropriate key while clicking to select multiple columns">
43 <options from_dataset="input1">
44 <column name="name" index="6"/>
45 <column name="value" index="6"/>
46 <filter type="unique_value" name="unique" column="6"/>
47 </options>
48 </param>
49 </when>
50 <when value="7">
51 <param name="feature" type="select" multiple="true" label="Extract features" help="Multi-select list - hold the appropriate key while clicking to select multiple columns">
52 <options from_dataset="input1">
53 <column name="name" index="7"/>
54 <column name="value" index="7"/>
55 <filter type="unique_value" name="unique" column="7"/>
56 </options>
57 </param>
58 </when>
59 </conditional>
60 </inputs>
61 <outputs>
62 <data format="input" name="out_file1" metadata_source="input1"/>
63 </outputs>
64 <tests>
65 <test>
66 <param name="input1" value="5.gff"/>
67 <param name="col" value="0" />
68 <param name="feature" value="chr5,chr6,chr7,chr8" />
69 <output name="out_file1" file="Extract_features1_out.gff"/>
70 </test>
71 </tests>
72 <help>
73
74 **What it does**
75
76 This tool extracts selected features from GFF data.
77
78 -----
79
80 **Example**
81
82 Selecting **promoter** from the following GFF data::
83
84 chr22 GeneA enhancer 10000000 10001000 500 + . TGA
85 chr22 GeneA promoter 10010000 10010100 900 + . TGA
86 chr22 GeneB promoter 10020000 10025000 400 - . TGB
87 chr22 GeneB CCDS2220 10030000 10065000 800 - . TGB
88
89 will produce the following output::
90
91 chr22 GeneA promoter 10010000 10010100 900 + . TGA
92 chr22 GeneB promoter 10020000 10025000 400 - . TGB
93
94 ----
95
96 .. class:: infomark
97
98 **About formats**
99
100 **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::
101
102 1. seqname - Must be a chromosome or scaffold.
103 2. source - The program that generated this feature.
104 3. feature - The name of this type of feature. Some examples of standard feature types are "CDS", "start_codon", "stop_codon", and "exon".
105 4. start - The starting position of the feature in the sequence. The first base is numbered 1.
106 5. end - The ending position of the feature (inclusive).
107 6. score - A score between 0 and 1000. If there is no score value, enter ".".
108 7. strand - Valid entries include '+', '-', or '.' (for don't know/care).
109 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 '.'.
110 9. group - All lines with the same group are linked together into a single item.
111
112
113 </help>
114 </tool>