Mercurial > repos > rnateam > ribotaper

comparison ribotaper_part1_create_annotation_files.xml @ 1:56ffbec351b3 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/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper/ commit 07674fe3507909d11d7431e3b8c48afcfb1f4b5e"
author rnateam
date Tue, 07 Jun 2022 09:22:45 +0000
parents bade631353d2
children
comparison
equal deleted inserted replaced
0:bade631353d2 1:56ffbec351b3
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[
11 #if $reference_genome.source == 'history':
12 #set $ref_genome = 'reference.fasta'
13 ln -s -f '${reference_genome.history_item}' $ref_genome &&
14 samtools faidx $ref_genome &&
15 #else:
16 #set $ref_genome = $reference_genome.index.fields.path
17 #end if
10 create_annotations_files.bash 18 create_annotations_files.bash
11 "$gtf" 19 '${gtf}'
12 "$fa" 20 '${ref_genome}'
13 "$ccdsid" 21 $ccdsid
14 "$appris" 22 $appris
15 "annotation_path" 23 './annotation_path'
16 && 24 &&
17 tar 25 tar czvf '${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"/>
69 </test>
70 <test expect_num_outputs="2">
71 <param name="gtf" value="test.gtf"/>
72 <conditional name="reference_genome">
73 <param name="source" value="indexed"/>
74 <param name="index" value="phix174"/>
75 </conditional>
76 <param name="ccdsid" value="true"/>
77 <param name="appris" value="true"/>
78 <output name="output1" file="annotation_path/start_stops_FAR_indexed.bed"/>
47 </test> 79 </test>
48 </tests> 80 </tests>
49 <help><![CDATA[ 81 <help><![CDATA[
50 Overview 82 Overview
51 -------- 83 --------
86 *Annotation_path* 118 *Annotation_path*
87 is used as an input for ``ribotaper part 3``. 119 is used as an input for ``ribotaper part 3``.
88 120
89 121
90 ]]></help> 122 ]]></help>
91 <citations> 123 <expand macro="citations"/>
92 <citation type="doi">10.1038/nmeth.3688</citation>
93 </citations>
94 </tool> 124 </tool>