Mercurial > repos > abims-sbr > gffalign

annotate GFFalign.xml @ 1:afed7e0cf69e draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/abims-sbr/tools-abims/tools/gffalign commit ca7b7864d099e092042f21d86cdc3c4552e54632"
author abims-sbr
date Fri, 08 Jan 2021 15:25:31 +0000
parents 294f5ba28746
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
294f5ba28746 "planemo upload for repository https://github.com/abims-sbr/tools-abims/tools/gffalign commit d8aa0e49353e78e5fd772498a1fcf591e2744f99"
abims-sbr
parents:
diff changeset
1 <tool id="gffalign" name="GFF align" version="0.1.0+galaxy0" python_template_version="3.5">
294f5ba28746 "planemo upload for repository https://github.com/abims-sbr/tools-abims/tools/gffalign commit d8aa0e49353e78e5fd772498a1fcf591e2744f99"
abims-sbr
parents:
diff changeset
2 <requirements>
294f5ba28746 "planemo upload for repository https://github.com/abims-sbr/tools-abims/tools/gffalign commit d8aa0e49353e78e5fd772498a1fcf591e2744f99"
abims-sbr
parents:
diff changeset
3 <requirement type="package" version="1.78">biopython</requirement>
294f5ba28746 "planemo upload for repository https://github.com/abims-sbr/tools-abims/tools/gffalign commit d8aa0e49353e78e5fd772498a1fcf591e2744f99"
abims-sbr
parents:
diff changeset
4 <requirement type="package" version="0.10.1">gffutils</requirement>
294f5ba28746 "planemo upload for repository https://github.com/abims-sbr/tools-abims/tools/gffalign commit d8aa0e49353e78e5fd772498a1fcf591e2744f99"
abims-sbr
parents:
diff changeset
5 </requirements>
294f5ba28746 "planemo upload for repository https://github.com/abims-sbr/tools-abims/tools/gffalign commit d8aa0e49353e78e5fd772498a1fcf591e2744f99"
abims-sbr
parents:
diff changeset
6 <command detect_errors="exit_code"><![CDATA[
294f5ba28746 "planemo upload for repository https://github.com/abims-sbr/tools-abims/tools/gffalign commit d8aa0e49353e78e5fd772498a1fcf591e2744f99"
abims-sbr
parents:
diff changeset
7 python3 '$__tool_directory__/GFFalign.py'
294f5ba28746 "planemo upload for repository https://github.com/abims-sbr/tools-abims/tools/gffalign commit d8aa0e49353e78e5fd772498a1fcf591e2744f99"
abims-sbr
parents:
diff changeset
8
294f5ba28746 "planemo upload for repository https://github.com/abims-sbr/tools-abims/tools/gffalign commit d8aa0e49353e78e5fd772498a1fcf591e2744f99"
abims-sbr
parents:
diff changeset
9 '$aln'
294f5ba28746 "planemo upload for repository https://github.com/abims-sbr/tools-abims/tools/gffalign commit d8aa0e49353e78e5fd772498a1fcf591e2744f99"
abims-sbr
parents:
diff changeset
10 '$queryGFF'
294f5ba28746 "planemo upload for repository https://github.com/abims-sbr/tools-abims/tools/gffalign commit d8aa0e49353e78e5fd772498a1fcf591e2744f99"
abims-sbr
parents:
diff changeset
11 '$targetGFF'
294f5ba28746 "planemo upload for repository https://github.com/abims-sbr/tools-abims/tools/gffalign commit d8aa0e49353e78e5fd772498a1fcf591e2744f99"
abims-sbr
parents:
diff changeset
12
294f5ba28746 "planemo upload for repository https://github.com/abims-sbr/tools-abims/tools/gffalign commit d8aa0e49353e78e5fd772498a1fcf591e2744f99"
abims-sbr
parents:
diff changeset
13 -m
294f5ba28746 "planemo upload for repository https://github.com/abims-sbr/tools-abims/tools/gffalign commit d8aa0e49353e78e5fd772498a1fcf591e2744f99"
abims-sbr
parents:
diff changeset
14 -t $t
294f5ba28746 "planemo upload for repository https://github.com/abims-sbr/tools-abims/tools/gffalign commit d8aa0e49353e78e5fd772498a1fcf591e2744f99"
abims-sbr
parents:
diff changeset
15 -v $v
294f5ba28746 "planemo upload for repository https://github.com/abims-sbr/tools-abims/tools/gffalign commit d8aa0e49353e78e5fd772498a1fcf591e2744f99"
abims-sbr
parents:
diff changeset
16 #if $extract.extract_fasta == 'true'
294f5ba28746 "planemo upload for repository https://github.com/abims-sbr/tools-abims/tools/gffalign commit d8aa0e49353e78e5fd772498a1fcf591e2744f99"
abims-sbr
parents:
diff changeset
17 -e $e '$output_extract_fasta'
294f5ba28746 "planemo upload for repository https://github.com/abims-sbr/tools-abims/tools/gffalign commit d8aa0e49353e78e5fd772498a1fcf591e2744f99"
abims-sbr
parents:
diff changeset
18 #end if
294f5ba28746 "planemo upload for repository https://github.com/abims-sbr/tools-abims/tools/gffalign commit d8aa0e49353e78e5fd772498a1fcf591e2744f99"
abims-sbr
parents:
diff changeset
19
294f5ba28746 "planemo upload for repository https://github.com/abims-sbr/tools-abims/tools/gffalign commit d8aa0e49353e78e5fd772498a1fcf591e2744f99"
abims-sbr
parents:
diff changeset
20 > '$output_file'
294f5ba28746 "planemo upload for repository https://github.com/abims-sbr/tools-abims/tools/gffalign commit d8aa0e49353e78e5fd772498a1fcf591e2744f99"
abims-sbr
parents:
diff changeset
21 ]]></command>
294f5ba28746 "planemo upload for repository https://github.com/abims-sbr/tools-abims/tools/gffalign commit d8aa0e49353e78e5fd772498a1fcf591e2744f99"
abims-sbr
parents:
diff changeset
22 <inputs>
294f5ba28746 "planemo upload for repository https://github.com/abims-sbr/tools-abims/tools/gffalign commit d8aa0e49353e78e5fd772498a1fcf591e2744f99"
abims-sbr
parents:
diff changeset
23 <param name="aln" type="data" format="tabular" label="Alignement file" help="Alignment file in TAB format. The suggested way to obtain it is to run Last and than convert the file from MAF to TAB with maf-convert" />
294f5ba28746 "planemo upload for repository https://github.com/abims-sbr/tools-abims/tools/gffalign commit d8aa0e49353e78e5fd772498a1fcf591e2744f99"
abims-sbr
parents:
diff changeset
24 <param name="queryGFF" type="data" format="gff" label="Query organism GFF file" help="Gff file of the query organism. The gene IDs in the GFF must be unique. To solve the problem please extract only the 'gene' lines. Try to format the file with AWK: awk `{if ($3==\'gene\') print $0}` GFFfile" />
294f5ba28746 "planemo upload for repository https://github.com/abims-sbr/tools-abims/tools/gffalign commit d8aa0e49353e78e5fd772498a1fcf591e2744f99"
abims-sbr
parents:
diff changeset
25 <param name="targetGFF" type="data" format="gff" label="Target organism GFF file" help="Gff file of the 'target' organism. The gene IDs in the GFF must be unique. To solve the problem please extract only the gene lines as explained in queryGff" />
294f5ba28746 "planemo upload for repository https://github.com/abims-sbr/tools-abims/tools/gffalign commit d8aa0e49353e78e5fd772498a1fcf591e2744f99"
abims-sbr
parents:
diff changeset
26
294f5ba28746 "planemo upload for repository https://github.com/abims-sbr/tools-abims/tools/gffalign commit d8aa0e49353e78e5fd772498a1fcf591e2744f99"
abims-sbr
parents:
diff changeset
27 <!--<param argument="-m" type="boolean" checked="false" truevalue="-memory" falsevalue="" label="Memory" help="Create an in-memory database. This option can't be used with the other DB options. Probably usefull in Galaxy integration" />-->
294f5ba28746 "planemo upload for repository https://github.com/abims-sbr/tools-abims/tools/gffalign commit d8aa0e49353e78e5fd772498a1fcf591e2744f99"
abims-sbr
parents:
diff changeset
28 <param argument="-t" type="integer" value="30" label="Interval" help="Interval, in nucleotide, within a gene is considered in the same position." />
294f5ba28746 "planemo upload for repository https://github.com/abims-sbr/tools-abims/tools/gffalign commit d8aa0e49353e78e5fd772498a1fcf591e2744f99"
abims-sbr
parents:
diff changeset
29 <param argument="-v" type="select" multiple="true" label="Verbosity" help="Output options. If not specify the software shows only the genes that are in the exact position of the genes in the target. It's possible to show annotated genes that are in aligned regions but that have different lengths or in slightly different positions. It's possible to select multiple values." >
294f5ba28746 "planemo upload for repository https://github.com/abims-sbr/tools-abims/tools/gffalign commit d8aa0e49353e78e5fd772498a1fcf591e2744f99"
abims-sbr
parents:
diff changeset
30 <option value="All">All</option>
294f5ba28746 "planemo upload for repository https://github.com/abims-sbr/tools-abims/tools/gffalign commit d8aa0e49353e78e5fd772498a1fcf591e2744f99"
abims-sbr
parents:
diff changeset
31 <option value="shorter">Shorter</option>
294f5ba28746 "planemo upload for repository https://github.com/abims-sbr/tools-abims/tools/gffalign commit d8aa0e49353e78e5fd772498a1fcf591e2744f99"
abims-sbr
parents:
diff changeset
32 <option value="longer">Longer</option>
294f5ba28746 "planemo upload for repository https://github.com/abims-sbr/tools-abims/tools/gffalign commit d8aa0e49353e78e5fd772498a1fcf591e2744f99"
abims-sbr
parents:
diff changeset
33 <option value="offset">Offset</option>
294f5ba28746 "planemo upload for repository https://github.com/abims-sbr/tools-abims/tools/gffalign commit d8aa0e49353e78e5fd772498a1fcf591e2744f99"
abims-sbr
parents:
diff changeset
34 <option value="new" selected="true">New</option>
294f5ba28746 "planemo upload for repository https://github.com/abims-sbr/tools-abims/tools/gffalign commit d8aa0e49353e78e5fd772498a1fcf591e2744f99"
abims-sbr
parents:
diff changeset
35 <option value="confirmed">Confirmed</option>
294f5ba28746 "planemo upload for repository https://github.com/abims-sbr/tools-abims/tools/gffalign commit d8aa0e49353e78e5fd772498a1fcf591e2744f99"
abims-sbr
parents:
diff changeset
36 </param>
294f5ba28746 "planemo upload for repository https://github.com/abims-sbr/tools-abims/tools/gffalign commit d8aa0e49353e78e5fd772498a1fcf591e2744f99"
abims-sbr
parents:
diff changeset
37 <conditional name="extract">
294f5ba28746 "planemo upload for repository https://github.com/abims-sbr/tools-abims/tools/gffalign commit d8aa0e49353e78e5fd772498a1fcf591e2744f99"
abims-sbr
parents:
diff changeset
38 <param name="extract_fasta" type="select" label="Extract fasta sequence of the new suggested gene" help="This option needs the fasta file of the genome. This will slow down the process A LOT.">
294f5ba28746 "planemo upload for repository https://github.com/abims-sbr/tools-abims/tools/gffalign commit d8aa0e49353e78e5fd772498a1fcf591e2744f99"
abims-sbr
parents:
diff changeset
39 <option value="true">Extract fasta sequence</option>
294f5ba28746 "planemo upload for repository https://github.com/abims-sbr/tools-abims/tools/gffalign commit d8aa0e49353e78e5fd772498a1fcf591e2744f99"
abims-sbr
parents:
diff changeset
40 <option selected="true" value="false">Do not extract fasta sequence</option>
294f5ba28746 "planemo upload for repository https://github.com/abims-sbr/tools-abims/tools/gffalign commit d8aa0e49353e78e5fd772498a1fcf591e2744f99"
abims-sbr
parents:
diff changeset
41 </param>
294f5ba28746 "planemo upload for repository https://github.com/abims-sbr/tools-abims/tools/gffalign commit d8aa0e49353e78e5fd772498a1fcf591e2744f99"
abims-sbr
parents:
diff changeset
42 <when value="true">
294f5ba28746 "planemo upload for repository https://github.com/abims-sbr/tools-abims/tools/gffalign commit d8aa0e49353e78e5fd772498a1fcf591e2744f99"
abims-sbr
parents:
diff changeset
43 <param argument="-e" type="data" format="fasta" label="Fasta file of the genome."/>
294f5ba28746 "planemo upload for repository https://github.com/abims-sbr/tools-abims/tools/gffalign commit d8aa0e49353e78e5fd772498a1fcf591e2744f99"
abims-sbr
parents:
diff changeset
44 </when>
294f5ba28746 "planemo upload for repository https://github.com/abims-sbr/tools-abims/tools/gffalign commit d8aa0e49353e78e5fd772498a1fcf591e2744f99"
abims-sbr
parents:
diff changeset
45 <when value="false"/>
294f5ba28746 "planemo upload for repository https://github.com/abims-sbr/tools-abims/tools/gffalign commit d8aa0e49353e78e5fd772498a1fcf591e2744f99"
abims-sbr
parents:
diff changeset
46 </conditional>
294f5ba28746 "planemo upload for repository https://github.com/abims-sbr/tools-abims/tools/gffalign commit d8aa0e49353e78e5fd772498a1fcf591e2744f99"
abims-sbr
parents:
diff changeset
47 </inputs>
294f5ba28746 "planemo upload for repository https://github.com/abims-sbr/tools-abims/tools/gffalign commit d8aa0e49353e78e5fd772498a1fcf591e2744f99"
abims-sbr
parents:
diff changeset
48 <outputs>
294f5ba28746 "planemo upload for repository https://github.com/abims-sbr/tools-abims/tools/gffalign commit d8aa0e49353e78e5fd772498a1fcf591e2744f99"
abims-sbr
parents:
diff changeset
49 <data name="output_file" format="gff" label="GFF align from ${on_string}"/>
294f5ba28746 "planemo upload for repository https://github.com/abims-sbr/tools-abims/tools/gffalign commit d8aa0e49353e78e5fd772498a1fcf591e2744f99"
abims-sbr
parents:
diff changeset
50 <data name="output_extract_fasta" format="fasta" label="Extracted fasta sequence from ${on_string}">
1
afed7e0cf69e "planemo upload for repository https://github.com/abims-sbr/tools-abims/tools/gffalign commit ca7b7864d099e092042f21d86cdc3c4552e54632"
abims-sbr
parents: 0
diff changeset
51 <filter>extract['extract_fasta'] == 'true'</filter>
0
294f5ba28746 "planemo upload for repository https://github.com/abims-sbr/tools-abims/tools/gffalign commit d8aa0e49353e78e5fd772498a1fcf591e2744f99"
abims-sbr
parents:
diff changeset
52 </data>
294f5ba28746 "planemo upload for repository https://github.com/abims-sbr/tools-abims/tools/gffalign commit d8aa0e49353e78e5fd772498a1fcf591e2744f99"
abims-sbr
parents:
diff changeset
53 </outputs>
294f5ba28746 "planemo upload for repository https://github.com/abims-sbr/tools-abims/tools/gffalign commit d8aa0e49353e78e5fd772498a1fcf591e2744f99"
abims-sbr
parents:
diff changeset
54
294f5ba28746 "planemo upload for repository https://github.com/abims-sbr/tools-abims/tools/gffalign commit d8aa0e49353e78e5fd772498a1fcf591e2744f99"
abims-sbr
parents:
diff changeset
55 <tests>
294f5ba28746 "planemo upload for repository https://github.com/abims-sbr/tools-abims/tools/gffalign commit d8aa0e49353e78e5fd772498a1fcf591e2744f99"
abims-sbr
parents:
diff changeset
56 <test>
294f5ba28746 "planemo upload for repository https://github.com/abims-sbr/tools-abims/tools/gffalign commit d8aa0e49353e78e5fd772498a1fcf591e2744f99"
abims-sbr
parents:
diff changeset
57 <param name="aln" value="genome_aln.tab" ftype="tabular"/>
294f5ba28746 "planemo upload for repository https://github.com/abims-sbr/tools-abims/tools/gffalign commit d8aa0e49353e78e5fd772498a1fcf591e2744f99"
abims-sbr
parents:
diff changeset
58 <param name="queryGFF" value="query.gff" ftype="gff"/>
294f5ba28746 "planemo upload for repository https://github.com/abims-sbr/tools-abims/tools/gffalign commit d8aa0e49353e78e5fd772498a1fcf591e2744f99"
abims-sbr
parents:
diff changeset
59 <param name="targetGFF" value="target.gff" ftype="gff"/>
294f5ba28746 "planemo upload for repository https://github.com/abims-sbr/tools-abims/tools/gffalign commit d8aa0e49353e78e5fd772498a1fcf591e2744f99"
abims-sbr
parents:
diff changeset
60 <param name="t" value="30"/>
294f5ba28746 "planemo upload for repository https://github.com/abims-sbr/tools-abims/tools/gffalign commit d8aa0e49353e78e5fd772498a1fcf591e2744f99"
abims-sbr
parents:
diff changeset
61 <param name="v" value="new"/>
294f5ba28746 "planemo upload for repository https://github.com/abims-sbr/tools-abims/tools/gffalign commit d8aa0e49353e78e5fd772498a1fcf591e2744f99"
abims-sbr
parents:
diff changeset
62 <output name="output_file" file="output.gff" ftype="gff"/>
294f5ba28746 "planemo upload for repository https://github.com/abims-sbr/tools-abims/tools/gffalign commit d8aa0e49353e78e5fd772498a1fcf591e2744f99"
abims-sbr
parents:
diff changeset
63 </test>
294f5ba28746 "planemo upload for repository https://github.com/abims-sbr/tools-abims/tools/gffalign commit d8aa0e49353e78e5fd772498a1fcf591e2744f99"
abims-sbr
parents:
diff changeset
64 </tests>
294f5ba28746 "planemo upload for repository https://github.com/abims-sbr/tools-abims/tools/gffalign commit d8aa0e49353e78e5fd772498a1fcf591e2744f99"
abims-sbr
parents:
diff changeset
65
294f5ba28746 "planemo upload for repository https://github.com/abims-sbr/tools-abims/tools/gffalign commit d8aa0e49353e78e5fd772498a1fcf591e2744f99"
abims-sbr
parents:
diff changeset
66 <help><![CDATA[
294f5ba28746 "planemo upload for repository https://github.com/abims-sbr/tools-abims/tools/gffalign commit d8aa0e49353e78e5fd772498a1fcf591e2744f99"
abims-sbr
parents:
diff changeset
67 Tool to extract genes coordinates from a whole genome alignment.
294f5ba28746 "planemo upload for repository https://github.com/abims-sbr/tools-abims/tools/gffalign commit d8aa0e49353e78e5fd772498a1fcf591e2744f99"
abims-sbr
parents:
diff changeset
68 This script needs an alignement in TAB format and two gff files.
294f5ba28746 "planemo upload for repository https://github.com/abims-sbr/tools-abims/tools/gffalign commit d8aa0e49353e78e5fd772498a1fcf591e2744f99"
abims-sbr
parents:
diff changeset
69 ]]></help>
294f5ba28746 "planemo upload for repository https://github.com/abims-sbr/tools-abims/tools/gffalign commit d8aa0e49353e78e5fd772498a1fcf591e2744f99"
abims-sbr
parents:
diff changeset
70 <citations>
294f5ba28746 "planemo upload for repository https://github.com/abims-sbr/tools-abims/tools/gffalign commit d8aa0e49353e78e5fd772498a1fcf591e2744f99"
abims-sbr
parents:
diff changeset
71 <citation type="bibtex">@manual{title="https://github.com/eosc-life/D4_marine_eukaryote_genomics_portal", url="https://github.com/eosc-life/D4_marine_eukaryote_genomics_portal"}</citation>
294f5ba28746 "planemo upload for repository https://github.com/abims-sbr/tools-abims/tools/gffalign commit d8aa0e49353e78e5fd772498a1fcf591e2744f99"
abims-sbr
parents:
diff changeset
72 </citations>
294f5ba28746 "planemo upload for repository https://github.com/abims-sbr/tools-abims/tools/gffalign commit d8aa0e49353e78e5fd772498a1fcf591e2744f99"
abims-sbr
parents:
diff changeset
73 </tool>