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comparison ribotaper_part1_create_annotation_files.xml @ 3:579b3be2559f draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper/ commit cd589d3c7c1bbe02e924f73475156c4f140d2fe2"
author rnateam
date Fri, 03 Jun 2022 20:17:28 +0000
parents 9dda0cc9ff98
children 74b0ca4446af
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2:9dda0cc9ff98 3:579b3be2559f
1 <tool id="ribotaper_create_annotation" name="ribotaper part 1: creation of annotation files" version="0.1.0"> 1 <tool id="ribotaper_create_annotation" name="ribotaper part 1: creation of annotation files" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile='20.01'>
2 <requirements> 2 <macros>
3 <requirement type="package" version="1.3.1a">ribotaper</requirement> 3 <import>macros.xml</import>
4 </requirements> 4 </macros>
5 <expand macro='bio_tools'/>
6 <expand macro='requirements'/>
5 <stdio> 7 <stdio>
6 <exit_code range="1:" /> 8 <exit_code range="1:"/>
7 </stdio> 9 </stdio>
8
9 <command><![CDATA[ 10 <command><![CDATA[
10 create_annotations_files.bash 11 #if $reference_genome.source == 'history':
11 "$gtf" 12 #set $ref_genome = 'reference.fasta'
12 "$fa" 13 ln -s -f '${reference_genome.history_item}' $ref_genome
13 "$ccdsid" 14 && samtools faidx $ref_genome
14 "$appris" 15 #else:
15 "annotation_path" 16 #set $ref_genome = $reference_genome.index.fields.path
17 #end if
18 && create_annotations_files.bash
19 '${gtf}'
20 '${ref_genome}'
21 $ccdsid
22 $appris
23 './annotation_path'
16 && 24 &&
17 tar 25 tar czvf '${output2}' './annotation_path'
18 "czvf"
19 "$output2"
20 "annotation_path"
21 26
22 ]]></command> 27 ]]></command>
23 <inputs> 28 <inputs>
24 <param name="gtf" type="data" format="GTF" label="GTF" 29 <param name="gtf" type="data" format="GTF" label="Annotation file"
25 help="GTF should contain: 30 help="The GTF file should contain: 1) coding and non-coding genes, 2) a 'transcript_id' and a 'gene_id' field for each 'exon' and 'CDS' row."/>
26 1) coding and non-coding genes, 2) a 'transcript_id' and a 'gene_id' field for each 'exon' and 'CDS' row. 31 <conditional name="reference_genome">
27 "/> 32 <param name="source" type="select" label="Source for the genome" help="Built-in references were created using default options.">
28 <param name="fa" type="data" format="fasta" label="Genome fasta file" help="FASTA-format, indexed and not repeat masked."/> 33 <option value="indexed" selected="true">Use a built-in genome</option>
29 <param name="ccdsid" type="boolean" falsevalue="false" truevalue="true" checked="true" label="Use ccdsid? (valid for Human Gencode 19 and Mouse Gencode M3 )" 34 <option value="history">Use a genome from history</option>
30 help="If yes, only exons/transcripts with the CCDS tag will be used as CCDS exons/transcripts, otherwise all exons/transcripts with a CDS region are going to be annotated as CCDS. 35 </param>
31 "/> 36 <when value="indexed">
32 <param name="appris" type="boolean" falsevalue="false" truevalue="true" checked="true" label="Use appris? (valid for Human Gencode 19 and Mouse Gencode M3 )" 37 <param name="index" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact the Galaxy team.">
33 help=" If yes, only exons/transcripts with the appris tag will be used, using only 1 transcript per appris gene (the appris_principal transcript or other appris transcript). If a gene does not have appris transcript, all the annotated transcript structures are used. 38 <options from_data_table="fasta_indexes">
34 "/> 39 <filter type="sort_by" column="2" />
40 <validator type="no_options" message="No genomes are available for the selected input dataset" />
41 </options>
42 </param>
43 </when>
44 <when value="history">
45 <param name="history_item" type="data" format="fasta" label="Reference genome" help="A reference genome in FASTA format" />
46 </when>
47 </conditional>
48 <param name="ccdsid" type="boolean" falsevalue="false" truevalue="true" checked="true"
49 label="Use CCDS annotation (valid for Human Gencode 19 and Mouse Gencode M3)"
50 help="If yes, only exons/transcripts with the CCDS tag will be used as CCDS exons/transcripts, otherwise all exons/transcripts with a CDS region are going to be annotated as CCDS."/>
51 <param name="appris" type="boolean" falsevalue="false" truevalue="true" checked="true" label="Use Appris annotation (valid for Human Gencode 19 and Mouse Gencode M3)"
52 help=" If yes, only exons/transcripts with the appris tag will be used, using only 1 transcript per appris gene (the appris_principal transcript or other appris transcript).
53 If a gene does not have appris transcript, all the annotated transcript structures are used."/>
35 </inputs> 54 </inputs>
36 <outputs> 55 <outputs>
37 <data name="output1" format="bed" from_work_dir="annotation_path/start_stops_FAR.bed" label="start_stops_FAR"/> 56 <data name="output1" format="bed" from_work_dir="annotation_path/start_stops_FAR.bed" label="${tool.name} on ${on_string}: start_stops FAR"/>
38 <data name="output2" format="tar" label="annotation_path"/> 57 <data name="output2" format="tgz" label="${tool.name} on ${on_string}: Annotation path"/>
39 </outputs> 58 </outputs>
40 <tests> 59 <tests>
41 <test> 60 <test expect_num_outputs="2">
42 <param name="gtf" value="test.gtf"/> 61 <param name="gtf" value="test.gtf"/>
43 <param name="fa" value="test.fa"/> 62 <conditional name="reference_genome">
63 <param name="source" value="history"/>
64 <param name="history_item" value="test.fa"/>
65 </conditional>
44 <param name="ccdsid" value="true"/> 66 <param name="ccdsid" value="true"/>
45 <param name="appris" value="true"/> 67 <param name="appris" value="true"/>
46 <output name="output1" file="annotation_path/start_stops_FAR.bed"/> 68 <output name="output1" file="annotation_path/start_stops_FAR.bed"/>
47 </test> 69 </test>
48 </tests> 70 </tests>
86 *Annotation_path* 108 *Annotation_path*
87 is used as an input for ``ribotaper part 3``. 109 is used as an input for ``ribotaper part 3``.
88 110
89 111
90 ]]></help> 112 ]]></help>
91 <citations> 113 <expand macro="citations"/>
92 <citation type="doi">10.1038/nmeth.3688</citation>
93 </citations>
94 </tool> 114 </tool>