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planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
author earlhaminst
date Wed, 15 Mar 2017 20:18:57 -0400
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1 <tool id="gstf_preparation" name="GeneSeqToFamily preparation" version="0.3.0">
2 <description>converts data for the workflow</description>
3 <command detect_errors="exit_code">
4 <![CDATA[
5 python '$__tool_directory__/gstf_preparation.py'
6 #for $q in $queries
7 --gff3 '${q.genome}:${q.gff3_input}'
8 #end for
9 #if str($json) != 'None'
10 #for $v in $json
11 --json '$v'
12 #end for
13 #end if
14 #for $fasta_input in $fasta_inputs
15 --fasta '${fasta_input}'
16 #end for
17 -o '$output_db'
18 --of '$output_fasta'
19 ]]>
20 </command>
21
22 <inputs>
23 <repeat name="queries" title="GFF3 dataset">
24 <param name="gff3_input" type="data" format="gff3" label="GFF3 dataset" />
25 <param name="genome" type="text" label="Genome name" help="Genome name without whitespaces or special characters">
26 <validator type="empty_field" />
27 </param>
28 </repeat>
29 <param name="json" type="data" format="json" multiple="true" optional="true" label="Gene features in JSON format generated by 'Get features by Ensembl ID' tool" />
30 <param name="fasta_inputs" type="data" format="fasta" multiple="true" label="Corresponding FASTA datasets" help="Each FASTA header line should start with a transcript id" />
31 </inputs>
32
33 <outputs>
34 <data name="output_db" format="sqlite" label="${tool.name} on ${on_string}: SQLite" />
35 <data name="output_fasta" format="fasta" label="${tool.name} on ${on_string}: FASTA" />
36 </outputs>
37
38 <tests>
39 <test>
40 <param name="fasta_inputs" ftype="fasta" value="Caenorhabditis_elegans.WBcel235.cds.all.shortened.fa" />
41 <param name="gff3_input" ftype="gff3" value="Caenorhabditis_elegans.WBcel235.87.chromosome.I.shortened.gff3" />
42 <param name="genome" value="caenorhabditis_elegans" />
43 <output name="output_db" file="test1.sqlite" compare="sim_size" />
44 <output name="output_fasta" file="test1.fasta" />
45 </test>
46 <test>
47 <param name="fasta_inputs" ftype="fasta" value="CDS.fasta" />
48 <param name="json" ftype="json" value="gene.json" />
49
50 <output name="output_db" file="test2.sqlite" compare="sim_size" />
51 <output name="output_fasta" file="test2.fasta" />
52 </test>
53 </tests>
54 <help>
55 <![CDATA[
56 **What it does**
57
58 This tool converts a set of GFF3 and/or JSON gene feature information datasets into SQLite format and modify the header lines of a corresponding CDS FASTA to be used with the GeneSeqToFamily workflow.
59
60 Example GFF3 file::
61
62 scaffold_0 MYZPE13164_Clone_G006_v1.0 gene 44968 69413 . - . ID=MYZPE13164_G006_v1.0_000000030;Name=MYZPE13164_G006_v1.0_000000030;biotype=protein_coding
63 scaffold_0 MYZPE13164_Clone_G006_v1.0 mRNA 44968 69413 . - . ID=MYZPE13164_G006_v1.0_000000030.1;Parent=MYZPE13164_G006_v1.0_000000030;Name=MYZPE13164_G006_v1.0_000000030.1;biotype=protein_coding;_AED=0.31
64 scaffold_0 MYZPE13164_Clone_G006_v1.0 three_prime_utr 44968 46637 . - . ID=MYZPE13164_G006_v1.0_000000030.1.3utr1;Parent=MYZPE13164_G006_v1.0_000000030.1
65 scaffold_0 MYZPE13164_Clone_G006_v1.0 exon 44968 47432 . - . ID=MYZPE13164_G006_v1.0_000000030.1.exon1;Parent=MYZPE13164_G006_v1.0_000000030.1
66 scaffold_0 MYZPE13164_Clone_G006_v1.0 CDS 46638 47432 . - 0 ID=MYZPE13164_G006_v1.0_000000030.1.cds1;Parent=MYZPE13164_G006_v1.0_000000030.1
67 scaffold_0 MYZPE13164_Clone_G006_v1.0 exon 53325 53539 . - . ID=MYZPE13164_G006_v1.0_000000030.1.exon2;Parent=MYZPE13164_G006_v1.0_000000030.1
68 scaffold_0 MYZPE13164_Clone_G006_v1.0 CDS 53325 53539 . - 2 ID=MYZPE13164_G006_v1.0_000000030.1.cds2;Parent=MYZPE13164_G006_v1.0_000000030.1
69 scaffold_0 MYZPE13164_Clone_G006_v1.0 exon 54614 54719 . - . ID=MYZPE13164_G006_v1.0_000000030.1.exon3;Parent=MYZPE13164_G006_v1.0_000000030.1
70 scaffold_0 MYZPE13164_Clone_G006_v1.0 CDS 54614 54719 . - 0 ID=MYZPE13164_G006_v1.0_000000030.1.cds3;Parent=MYZPE13164_G006_v1.0_000000030.1
71 scaffold_0 MYZPE13164_Clone_G006_v1.0 CDS 54852 55106 . - 0 ID=MYZPE13164_G006_v1.0_000000030.1.cds4;Parent=MYZPE13164_G006_v1.0_000000030.1
72 scaffold_0 MYZPE13164_Clone_G006_v1.0 exon 54852 55117 . - . ID=MYZPE13164_G006_v1.0_000000030.1.exon4;Parent=MYZPE13164_G006_v1.0_000000030.1
73 scaffold_0 MYZPE13164_Clone_G006_v1.0 five_prime_utr 55107 55117 . - . ID=MYZPE13164_G006_v1.0_000000030.1.5utr1;Parent=MYZPE13164_G006_v1.0_000000030.1
74 scaffold_0 MYZPE13164_Clone_G006_v1.0 five_prime_utr 68851 69413 . - . ID=MYZPE13164_G006_v1.0_000000030.1.5utr2;Parent=MYZPE13164_G006_v1.0_000000030.1
75 scaffold_0 MYZPE13164_Clone_G006_v1.0 exon 68851 69413 . - . ID=MYZPE13164_G006_v1.0_000000030.1.exon5;Parent=MYZPE13164_G006_v1.0_000000030.1
76
77 The following features are parsed: **gene**, **mRNA**, **transcript**, **exon**, **five_prime_utr**, **three_prime_utr** and **CDS**, all other are ignored. Also, **ID** and **Parent** tags are needed to create relations.
78 ]]>
79 </help>
80 <citations>
81 </citations>
82 </tool>