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planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/fromgtfTobed12 commit 15b8c2cc83708044413a152322bcbfca8a74d29a
author lldelisle
date Fri, 03 Nov 2023 14:13:51 +0000
parents 418e4d0fe0bd
children
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0:418e4d0fe0bd 1:6fd4b3b90220
1 <tool id="fromgtfTobed12" name="fromgtftobed12" version="0.11.1+galaxy0"> 1 <tool id="fromgtfTobed12" name="fromgtftobed12" version="0.11.1+galaxy1">
2 <description> Convert a gtf to a bed12.</description> 2 <description> Convert a gtf to a bed12.</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="0.11.1">gffutils</requirement> 4 <requirement type="package" version="0.11.1">gffutils</requirement>
5 </requirements> 5 </requirements>
6 <stdio> 6 <stdio>
12 <regex match="Exception:" /> 12 <regex match="Exception:" />
13 </stdio> 13 </stdio>
14 <command> 14 <command>
15 <![CDATA[ 15 <![CDATA[
16 python3 $__tool_directory__/fromgtfTobed12.py 16 python3 $__tool_directory__/fromgtfTobed12.py
17 $useGene 17 #if str($preferedName) != "":
18 --preferedName $preferedName
19 #end if
18 $mergeTranscripts 20 $mergeTranscripts
19 $ucscformat 21 $ucscformat
20 --output $output 22 --output $output
21 $input 23 $input
22 ]]> 24 ]]>
23 </command> 25 </command>
24 <inputs> 26 <inputs>
25 <param name="input" multiple="false" type="data" format="gtf" label="Select the gtf to convert."/> 27 <param name="input" multiple="false" type="data" format="gtf" label="Select the gtf to convert."/>
26 <param argument="--useGene" type="boolean" checked="False" truevalue="--useGene" falsevalue="" label="Uses the gene name instead of the transcript name."/>
27 <param name="mergeTranscripts" type="select" label="Do you want to merge all transcripts of a gene in a single line?"> 28 <param name="mergeTranscripts" type="select" label="Do you want to merge all transcripts of a gene in a single line?">
28 <option value="" selected="true">No</option> 29 <option value="" selected="true">No</option>
29 <option value="--mergeTranscripts">Yes</option> 30 <option value="--mergeTranscripts">Yes</option>
30 <option value="--mergeTranscriptsAndOverlappingExons">Yes and merge overlapping exons</option> 31 <option value="--mergeTranscriptsAndOverlappingExons">Yes and merge overlapping exons</option>
31 </param> 32 </param>
33 <param argument="--preferedName" type="text" value="" label="Use a specific name for the 4th column" help="By default the 4th column will be transcript_name or gene_name if you merge transcripts. If you prefer 'gene_id', for example, then set this option." />
32 <param argument="--ucscformat" type="boolean" checked="True" truevalue="--ucscformat" falsevalue="" label="If you want that all chromosome names begin with 'chr'."/> 34 <param argument="--ucscformat" type="boolean" checked="True" truevalue="--ucscformat" falsevalue="" label="If you want that all chromosome names begin with 'chr'."/>
33 </inputs> 35 </inputs>
34 36
35 <outputs> 37 <outputs>
36 <data format="bed" name="output" label="$input.name as bed12"/> 38 <data format="bed" name="output" label="$input.name as bed12"/>
43 <output name="output" file="test.bed"/> 45 <output name="output" file="test.bed"/>
44 </test> 46 </test>
45 <test> 47 <test>
46 <param name="input" value="Homo_sapiens.GRCh38.95_491firstLines.gtf.gz"/> 48 <param name="input" value="Homo_sapiens.GRCh38.95_491firstLines.gtf.gz"/>
47 <param name="ucscformat" value="--ucscformat"/> 49 <param name="ucscformat" value="--ucscformat"/>
48 <param name="useGene" value="--useGene"/> 50 <param name="preferedName" value="gene_name"/>
49 <output name="output" file="testWithGenes.bed"/> 51 <output name="output" file="testWithGenes.bed"/>
50 </test> 52 </test>
51 <test> 53 <test>
52 <param name="input" value="Homo_sapiens.GRCh38.95_491firstLines.gtf.gz"/> 54 <param name="input" value="Homo_sapiens.GRCh38.95_491firstLines.gtf.gz"/>
55 <param name="ucscformat" value="--ucscformat"/>
56 <param name="preferedName" value="gene_id"/>
57 <output name="output" file="testWithGeneIds.bed"/>
58 </test>
59 <test>
60 <param name="input" value="Homo_sapiens.GRCh38.95_491firstLines.gtf.gz"/>
53 <param name="mergeTranscripts" value="--mergeTranscripts"/> 61 <param name="mergeTranscripts" value="--mergeTranscripts"/>
54 <param name="useGene" value="--useGene"/>
55 <param name="ucscformat" value=""/> 62 <param name="ucscformat" value=""/>
56 <output name="output" file="testMergeNotUCSC.bed"/> 63 <output name="output" file="testMergeNotUCSC.bed"/>
57 </test> 64 </test>
58 <test> 65 <test>
59 <param name="input" value="Homo_sapiens.GRCh38.95_491firstLines.gtf.gz"/> 66 <param name="input" value="Homo_sapiens.GRCh38.95_491firstLines.gtf.gz"/>
60 <param name="mergeTranscripts" value="--mergeTranscriptsAndOverlappingExons"/> 67 <param name="mergeTranscripts" value="--mergeTranscriptsAndOverlappingExons"/>
61 <param name="useGene" value="--useGene"/>
62 <param name="ucscformat" value=""/> 68 <param name="ucscformat" value=""/>
63 <output name="output" file="testMergeExons.bed"/> 69 <output name="output" file="testMergeExons.bed"/>
64 </test> 70 </test>
65 </tests> 71 </tests>
66 <help><![CDATA[ 72 <help><![CDATA[