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comparison gff3_extract_sequence.xml @ 4:34b80e483fb8 draft

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planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
author cpt
date Mon, 05 Jun 2023 02:43:58 +0000
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3:73390562b5a2 4:34b80e483fb8
1 <tool id="edu.tamu.cpt.gff3.export_seq" name="GFF3 Feature Sequence Export" version="19.1.0.0">
2 <description>Export corresponding sequence in genome from GFF3</description>
3 <macros>
4 <import>macros.xml</import>
5 <import>cpt-macros.xml</import>
6 </macros>
7 <expand macro="requirements"/>
8 <command detect_errors="aggressive"><![CDATA[
9 @GENOME_SELECTOR_PRE@
10
11 '$__tool_directory__/gff3_extract_sequence.py'
12 @GENOME_SELECTOR@
13
14 @INPUT_GFF@
15
16 #if $feature_filter and $feature_filter is not None:
17 --feature_filter '$feature_filter'
18 #end if
19 '$nodesc'
20 > '$default']]></command>
21 <inputs>
22 <expand macro="genome_selector"/>
23 <expand macro="gff3_input"/>
24 <param label="Filter for specific feature types" name="feature_filter" type="text" help="Use 'nice_cds' if your features are coming from Apollo, however this will fail on non-Apollo data"/>
25 <param label="Remove description (use if blasting)" name="nodesc" type="boolean" truevalue="--nodesc" falsevalue=""/>
26 </inputs>
27 <outputs>
28 <data format="fasta" hidden="false" name="default"/>
29 </outputs>
30 <tests>
31 <test>
32 <param name="reference_genome_source" value="history"/>
33 <param name="genome_fasta" value="T7_ExtSeqIn.fasta"/>
34 <param name="gff3_data" value="T7_ExtSeqIn.gff3"/>
35 <param name="nodesc" value=""/>
36 <param name="feature_filter" value="CDS"/>
37 <output name="output" file="T7_ExtSeqOut.fasta"/>
38 </test>
39 <test>
40 <param name="reference_genome_source" value="history"/>
41 <param name="genome_fasta" value="Miro_ExtSeqIn.fa"/>
42 <param name="gff3_data" value="Miro_ExtSeqIn.gff3"/>
43 <param name="nodesc" value=""/>
44 <param name="feature_filter" value="CDS"/>
45 <output name="output" file="Miro_ExtSeqOut1.fa"/>
46 </test>
47 <test>
48 <param name="reference_genome_source" value="history"/>
49 <param name="genome_fasta" value="Miro_ExtSeqIn.fa"/>
50 <param name="gff3_data" value="Miro_ExtSeqIn.gff3"/>
51 <param name="feature_filter" value="CDS"/>
52 <param name="nodesc" value="--nodesc"/>
53 <output name="output" file="Miro_ExtSeqOut2.fa"/>
54 </test>
55 </tests>
56 <help><![CDATA[
57 **What it does**
58
59 From the FASTA sequence for a genome, extracts the *nucleotide* sequences for
60 all CDSs in an input GFF3 and outputs them as a multi-FASTA formatted file.
61
62 The filter for specific feature types was designed for data retrieved from Apollo.
63 Using ‘unique_cds’ extracts the sequence for all CDS. Using ‘nice_cds’ will extract
64 the sequence only for CDS features with a start codon (recommended). If a gene from
65 Apollo has multiple CDSs, the tool will append a "_##" to the end of subsequent genes.
66
67 ]]></help>
68 <expand macro="citations"/>
69 </tool>